Molecular history of plague

Co-formulation of the rF1V plague vaccine with depot-formulated cytokines enhances immunogenicity and efficacy to elicit protective responses against aerosol challenge in mice

This study evaluated a depot-formulated cytokine-based adjuvant to improve the efficacy of the recombinant F1V (rF1V) plague vaccine and examined the protective response following aerosol challenge in a murine model. The results of this study showed that co-formulation of the Alhydrogel-adsorbed rF1V plague fusion vaccine with the depot-formulated cytokines recombinant human interleukin 2 (rhuIL-2) and/or recombinant murine granulocyte macrophage colony-stimulating factor (rmGM-CSF) significantly enhances immunogenicity and significant protection at lower antigen doses against a lethal aerosol challenge. These results provide additional support for the co-application of the depot-formulated IL-2 and/or GM-CSF cytokines to enhance vaccine efficacy.

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.

Whole-genome CRISPR screen identifies RAVER1 as a key regulator of RIPK1-mediated inflammatory cell death, PANoptosis

Transforming growth factor-β-activated kinase 1 (TAK1) is a central regulator of innate immunity, cell death, inflammation, and cellular homeostasis. Therefore, many pathogens carry TAK1 inhibitors (TAK1i). As a host strategy to counteract this, inhibition or deletion of TAK1 induces spontaneous inflammatory cell death, PANoptosis, through the RIPK1-PANoptosome complex, containing the NLRP3 inflammasome and caspase-8/FADD/RIPK3 as integral components; however, PANoptosis also promotes pathological inflammation. Therefore, understanding molecular mechanisms that regulate TAK1i-induced cell death is essential. Here, we report a genome-wide CRISPR screen in macrophages that identified TAK1i-induced cell death regulators, including polypyrimidine tract-binding (PTB) protein 1 (PTBP1), a known regulator of RIPK1, and a previously unknown regulator RAVER1. RAVER1 blocked alternative splicing of Ripk1, and its genetic depletion inhibited TAK1i-induced, RIPK1-mediated inflammasome activation and PANoptosis. Overall, our CRISPR screen identified several positive regulators of PANoptosis. Moreover, our study highlights the utility of genome-wide CRISPR-Cas9 screens in myeloid cells for comprehensive characterization of complex cell death pathways to discover therapeutic targets.

Global Catastrophic Biological Risks in the Post-COVID-19 World: Time to Act Is Now

Global Catastrophic Biological Risks (GCBRs) refer to events with biological agents that can result in unprecedented or catastrophic disasters that are beyond the collective response-abilities of nation-states and the existing governance instruments of global governance and international affairs. This article offers a narrative review, with a view to new hypothesis development to rethink GCBRs after coronavirus disease 2019 (COVID-19) so as to better prepare for future pandemics and ecological crises, if not to completely prevent them. To determine GCBRs' spatiotemporal contexts, define causality, impacts, differentiate the risk and the event, would improve theorization of GCBRs compared to the impact-centric current definition. This could in turn lead to improvements in preparedness, response, allocation of resources, and possibly deterrence, while actively discouraging lack of due biosecurity diligence. Critical governance of GCBRs in ways that unpack the political power-related dimensions could be particularly valuable because the future global catastrophic events might be different in quality, scale, and actors. Theorization of GCBRs remains an important task going forward in the 21st century in ways that draw from experiences in the field, while integrating flexibility, versatility, and critically informed responses to GCBRs.

Epidemiological Characteristics of Human and Animal Plague in Yunnan Province, China, 1950 to 2020

This study analyzed the epidemiological characteristics of 3,464 human plague cases and the distribution pattern of 4,968 Yersinia pestis isolates from humans, hosts, and vector insects from 1950 to 2020 among two natural plague foci in Yunnan Province, China. These foci include the Rattus flavipectus plague focus of the Yunnan, Guangdong, and Fujian provinces and the Apodemus chevrieri-Eothenomys miletus plague focus of the highlands of northwestern Yunnan Province. The case fatality rate for plague in humans was 18.39% (637/3,464), and the total isolation rate of Y. pestis was 0.17% (4,968/2,975,288). Despite that the frequency of human cases declined rapidly, the animal plague fluctuated greatly, alternating between activity and inactivity in these foci. The tendency among human cases can be divided into 4 stages, 1950 to 1955, 1956 to 1989, 1990 to 2005, and 2006 to 2020. Bubonic plague accounted for the majority of cases in Yunnan, where pneumonic and septicemic plague rarely occurred. The natural plague foci have been in a relatively active state due to the stability of local ecology. Dense human population and frequent contact with host animals contribute to the high risk of human infection. This study systematically analyzed the epidemic pattern of human plague and the distribution characteristics of Y. pestis in the natural plague foci in Yunnan, providing a scientific basis for further development and adjustment of plague prevention and control strategies. IMPORTANCE Yunnan is the origin of the third plague pandemic. The analysis of human and animal plague characteristics of plague foci in Yunnan enlightens the prevention and control of the next plague pandemics. The plague characteristics of Yunnan show that human plague occurred when animal plague reached a certain scale, and strengthened surveillance of animal plague and reducing the density of host animals and transmission vectors contribute to the prevention and control of human plague outbreaks. The phenomenon of alternation between the resting period and active period of plague foci in Yunnan further proves the endogenous preservation mechanism of plague.

The magnitude of the germinal center B cell and T follicular helper cell response predicts long-lasting antibody titers to plague vaccination

The development of a safe and effective vaccine against Yersinia pestis, the causative organism for plague disease, remains an important global health priority. Studies have demonstrated effective immune-based protection against plague challenge that is induced by plague antigen subunit vaccination in an aqueous alhydrogel formulation; however, whether these candidate vaccines in this formulation and presentation, induce long-lasting immunological memory in the form of durable cellular and antibody recall responses has not been fully demonstrated. In this study, we analyzed germinal center T follicular helper and germinal center B cell responses following F1V and F1 + V plague subunit immunization of mice with vaccines formulated in various adjuvants. Our data demonstrate that recombinant plague protein immunization formulated with IL-2/GM-CSF cytokines bound to alhydrogel adjuvant drive an increase in the magnitude of the germinal center T follicular helper and germinal center B cell responses following primary immunization, compared to vaccines formulated with Alhydrogel adjuvant alone. In contrast, plague protein subunit immunization combined with CpG ODN bound to alhydrogel increased the magnitude and duration of the germinal center Tfh and B cell responses following booster immunization. Importantly, enhanced germinal center Tfh and B cell responses correlated with long-lasting and high F1V-specific antibody titers and more robust antibody recall responses to F1V re-exposure. These findings indicate that vaccine formulations that drive enhancement of the germinal center Tfh and B cell responses are critical for inducing durable plague-specific humoral immunity.

Complete Protection Against Yersinia pestis in BALB/c Mouse Model Elicited by Immunization With Inhalable Formulations of rF1-V10 Fusion Protein via Aerosolized Intratracheal Inoculation

Pneumonic plague, caused by Yersinia pestis, is an infectious disease with high mortality rates unless treated early with antibiotics. Currently, no FDA-approved vaccine against plague is available for human use. The capsular antigen F1, the low-calcium-response V antigen (LcrV), and the recombinant fusion protein (rF1-LcrV) of Y. pestis are leading subunit vaccine candidates under intense investigation; however, the inability of recombinant antigens to provide complete protection against pneumonic plague in animal models remains a significant concern. In this study, we compared immunoprotection against pneumonic plague provided by rF1, rV10 (a truncation of LcrV), and rF1-V10, and vaccinations delivered via aerosolized intratracheal (i.t.) inoculation or subcutaneous (s.c.) injection. We further considered three vaccine formulations: conventional liquid, dry powder produced by spray freeze drying, or dry powder reconstituted in PBS. The main findings are: (i) rF1-V10 immunization with any formulation via i.t. or s.c. routes conferred 100% protection against Y. pestis i.t. infection; (ii) rF1 or rV10 immunization using i.t. delivery provided significantly stronger protection than rF1 or rV10 immunization via s.c. delivery; and (iii) powder formulations of subunit vaccines induced immune responses and provided protection equivalent to those elicited by unprocessed liquid formulations of vaccines. Our data indicate that immunization with a powder formulation of rF1-V10 vaccines via an i.t. route may be a promising vaccination strategy for providing protective immunity against pneumonic plague.

Wildlife in Cameroon harbor diverse coronaviruses, including many closely related to human coronavirus 229E

Zoonotic spillover of animal viruses into human populations is a continuous and increasing public health risk. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlights the global impact of emergence. Considering the history and diversity of coronaviruses (CoVs), especially in bats, SARS-CoV-2 will likely not be the last to spillover from animals into human populations. We sampled and tested wildlife in the Central African country Cameroon to determine which CoVs are circulating and how they relate to previously detected human and animal CoVs. We collected animal and ecological data at sampling locations and used family-level consensus PCR combined with amplicon sequencing for virus detection. Between 2003 and 2018, samples were collected from 6,580 animals of several different orders. CoV RNA was detected in 175 bats, a civet, and a shrew. The CoV RNAs detected in the bats represented 17 different genetic clusters, coinciding with alpha (n = 8) and beta (n = 9) CoVs. Sequences resembling human CoV-229E (HCoV-229E) were found in 40 Hipposideridae bats. Phylogenetic analyses place the human-derived HCoV-229E isolates closest to those from camels in terms of the S and N genes but closest to isolates from bats for the envelope, membrane, and RNA-dependent RNA polymerase genes. The CoV RNA positivity rate in bats varied significantly (P < 0.001) between the wet (8.2 per cent) and dry seasons (4.5 per cent). Most sampled species accordingly had a wet season high and dry season low, while for some the opposite was found. Eight of the suspected CoV species of which we detected RNA appear to be entirely novel CoV species, which suggests that CoV diversity in African wildlife is still rather poorly understood. The detection of multiple different variants of HCoV-229E-like viruses supports the bat reservoir hypothesis for this virus, with the phylogenetic results casting some doubt on camels as an intermediate host. The findings also support the previously proposed influence of ecological factors on CoV circulation, indicating a high level of underlying complexity to the viral ecology. These results indicate the importance of investing in surveillance activities among wild animals to detect all potential threats as well as sentinel surveillance among exposed humans to determine emerging threats.

Life after COVID-19: Future directions?

The humans’ vulnerability and fragility have been demonstrated during pandemics, and as a community, will need proper preparation. The coronavirus outbreak was first reported at the end of 2019 and declared a pandemic by the World Health Organization. Around the world, the response to the virus outbreak has been different.

The detection, traceability, and the response for different countries have been delayed, causing the overwhelming of the health systems. However, some other nations exercised various strategies to contain the infection’s dissemination and recorded a low number of cases. The different measures taken, including contact tracing, lockdown, case detection, social distancing, and quarantine strategies, helped control the disease’s spreading.

Only time will tell how well the world faced the outbreak. We also suggest the future directions that the global community should take to manage and mitigate the emergency.

Badania kopalnego DNA – możliwości i ograniczenia

Ostatnie cztery dekady przyniosły znaczący rozwój archeologii molekularnej i badania nad kopalnym DNA (aDNA). Nowatorskie metody uwzględniają szeroki zakres badań, począwszy od sekwencjonowania niewielkich fragmentów mitochondrialnego DNA po wielkoskalowe badania całych populacji, łączące sekwencjonowanie genomów mitochondrialnych, genów podlegających doborowi naturalnemu, jak i całych genomów jądrowych. Postęp, zwłaszcza w dziedzinie technologii sekwencjonowania DNA, umożliwił pozyskanie informacji ze szczątków paleontologicznych i materiału archeologicznego, umożliwiając zbadanie związków filogenetycznych między wymarłymi i współczesnymi gatunkami. Dzięki zastosowaniu technologii sekwencjonowania nowej generacji możliwe stało się poznanie sekwencji DNA nie tylko bezpośrednio ze szczątków ludzkich lub zwierzęcych, ale także z osadów sedymentacyjnych z głębin jezior oraz jaskiń. W artykule przedstawiono możliwości i ograniczenia występujące w badaniach nad kopalnym DNA ludzi, zwierząt czy bakterii z podkreśleniem wkładu polskich badaczy w rozwój tej dziedziny nauki.

Plague Prevention and Therapy: Perspectives on Current and Future Strategies

Plague, caused by the bacterial pathogen Yersinia pestis, is a vector-borne disease that has caused millions of human deaths over several centuries. Presently, human plague infections continue throughout the world. Transmission from one host to another relies mainly on infected flea bites, which can cause enlarged lymph nodes called buboes, followed by septicemic dissemination of the pathogen. Additionally, droplet inhalation after close contact with infected mammals can result in primary pneumonic plague. Here, we review research advances in the areas of vaccines and therapeutics for plague in context of Y. pestis virulence factors and disease pathogenesis. Plague continues to be both a public health threat and a biodefense concern and we highlight research that is important for infection mitigation and disease treatment.

Distribution and Characteristics of Human Plague Cases and Yersinia pestis Isolates from 4 Marmota Plague Foci, China, 1950-2019

We analyzed epidemiologic characteristics and distribution of 1,067 human plague cases and 5,958 Yersinia pestis isolates collected from humans, host animals, and insect vectors during 1950–2019 in 4 Marmota plague foci in China. The case-fatality rate for plague in humans was 68.88%; the overall trend slowly decreased over time but fluctuated greatly. Most human cases (98.31%) and isolates (82.06%) identified from any source were from the Marmota himalayana plague focus. The tendency among human cases could be divided into 3 stages: 1950–1969, 1970–2003, and 2004–2019. The Marmota sibirica plague focus has not had identified human cases nor isolates since 1926. However, in the other 3 foci, Y. pestis continues to circulate among animal hosts; ecologic factors might affect local Y. pestis activity. Marmota plague foci are active in China, and the epidemic boundary is constantly expanding, posing a potential threat to domestic and global public health.

Impact of Toll-Like Receptor-Specific Agonists on the Host Immune Response to the Yersinia pestis Plague rF1V Vaccine

Relatively recent advances in plague vaccinology have produced the recombinant fusion protein F1-V plague vaccine. This vaccine has been shown to readily protect mice from both bubonic and pneumonic plague. The protection afforded by this vaccine is solely based upon the immune response elicited by the F1 or V epitopes expressed on the F1-V fusion protein. Accordingly, questions remain surrounding its efficacy against infection with non-encapsulated (F1-negative) strains. In an attempt to further optimize the F1-V elicited immune response and address efficacy concerns, we examined the inclusion of multiple toll-like receptor agonists into vaccine regimens. We examined the resulting immune responses and also any protection afforded to mice that were exposed to aerosolized Yersinia pestis. Our data demonstrate that it is possible to further augment the F1-V vaccine strategy in order to optimize and augment vaccine efficacy.

The role of louse-transmitted diseases in historical plague pandemics

The rodent-murine ectoparasite-human model of plague transmission does not correspond with historical details around plague pandemics in Europe. New analysis of ancient genomes reveal that Yersinia pestis was unable to be transmitted by rat fleas until around 4000 Before Present, which challenges the rodent-murine ectoparasite-human model of plague transmission and historical details around plague pandemics in Europe. In this Review, we summarise data regarding Y pestis transmission by human lice in the context of genomic evolution and co-transmission of other major epidemic deadly pathogens throughout human history, with the aim of broadening our view of plague transmission. Experimental models support the efficiency of human lice as plague vectors through infected faeces, which suggest that Y pestis could be a louse-borne disease, similar to Borrelia recurrentis, Rickettsia prowazekii, and Bartonella quintana. Studies have shown that louse-borne outbreaks often involve multiple pathogens, and several cases of co-transmission of Y pestis and B quintana have been reported. Furthermore, an exclusive louse-borne bacterium, namely B recurrentis, was found to be circulating in northern Europe during the second plague pandemic (14th-18th century). Current data make it possible to attribute large historical pandemics to multiple bacteria, and suggests that human lice probably played a preponderant role in the interhuman transmission of plague and pathogen co-transmission during previous large epidemics, including plague pandemics.

A forensic evaluation of plague - a re-emerging infectious disease with biowarfare potential

Plague is an acute infectious disease caused by the gram-negative cocco-bacillus Yersinia pestis. It has been responsible for 200 million deaths throughout history with three major pandemics. There are three forms: bubonic, septicaemic and pneumonic, each carrying a significant mortality rate. The usual transmission is from fleas carried by rodents. Recently, it has been listed as one of the reemerging infectious diseases globally, with a potential use in bioterrorism. At autopsy there may be lymphadenopathy, fulminant pneumonia or diffuse interstitial pneumonitis. However any organ may be affected with myocarditis, meningitis, pharyngitis and hepatic and splenic necrosis. The lethality of plague with the resurgence in numbers of cases, development of antibiotic resistance, recent occurrence in urban areas and the lack of a vaccine make it a disease not to be missed in the mortuary.

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.

Google Trends Predicts Present and Future Plague Cases During the Plague Outbreak in Madagascar: Infodemiological Study

Background

Plague is a highly infectious zoonotic disease caused by the bacillus Yersinia pestis. Three major forms of the disease are known: bubonic, septicemic, and pneumonic plague. Though highly related to the past, plague still represents a global public health concern. Cases of plague continue to be reported worldwide. In recent months, pneumonic plague cases have been reported in Madagascar. However, despite such a long-standing and rich history, it is rather difficult to get a comprehensive overview of the general situation. Within the framework of electronic health (eHealth), in which people increasingly search the internet looking for health-related material, new information and communication technologies could enable researchers to get a wealth of data, which could complement traditional surveillance of infectious diseases.

Objective

In this study, we aimed to assess public reaction regarding the recent plague outbreak in Madagascar by quantitatively characterizing the public’s interest.

Methods

We captured public interest using Google Trends (GT) and correlated it to epidemiological real-world data in terms of incidence rate and spread pattern.

Results

Statistically significant positive correlations were found between GT search data and confirmed (R²=0.549), suspected (R²=0.265), and probable (R²=0.518) cases. From a geospatial standpoint, plague-related GT queries were concentrated in Toamasina (100%), Toliara (68%), and Antananarivo (65%). Concerning the forecasting models, the 1-day lag model was selected as the best regression model.

Conclusions

An earlier digital Web search reaction could potentially contribute to better management of outbreaks, for example, by designing ad hoc interventions that could contain the infection both locally and at the international level, reducing its spread.

Recovery of Bordetella bronchiseptica sequence type 82 and B. pseudohinzii from urban rats in Terengganu, Malaysia

Rodents have historically been associated with zoonotic pandemics that claimed the lives of large human populations. Appropriate pathogen surveillance initiatives could contribute to early detection of zoonotic infections to prevent future outbreaks. Bordetella species are bacteria known to cause mild to severe respiratory disease in mammals and, some have been described to infect, colonize and spread in rodents. There is a lack of information on the population diversity of bordetellae among Malaysian wild rodents. Here, bordetellae recovered from lung tissues of wild rats were genotypically characterized using 16S rDNA sequencing, MLST and nrdA typing. A novel B. bronchiseptica ST82, closely related to other human-derived isolates, was discovered in three wild rats (n=3) from Terengganu (5.3333° N, 103.1500° E). B. pseudohinzii, a recently identified laboratory mice inhabitant, was also recovered from one rat (n=1). Both bordetellae displayed identical antimicrobial resistance profiles, indicating the close phylogenetic association between them. Genotyping using the 765-bp nrdA locus was shown to be compatible with the MLST-based phylogeny, with the added advantage of being able to genotype non-classical bordetellae. The recovery of B. pseudohinzii from wild rat implied that this bordetellae has a wider host range than previously thought. The findings from this study suggest that bordetellae surveillance among wild rats in Malaysia has to be continued and expanded to other states to ensure early identification of species capable of causing public health disorder.