Can we make human plague history? A call to action

Yersiniomics, a Multi-Omics Interactive Database for Yersinia Species

The genus Yersinia includes a large variety of nonpathogenic and life-threatening pathogenic bacteria, which cause a broad spectrum of diseases in humans and animals, such as plague, enteritis, Far East scarlet-like fever (FESLF), and enteric redmouth disease. Like most clinically relevant microorganisms, Yersinia spp. are currently subjected to intense multi-omics investigations whose numbers have increased extensively in recent years, generating massive amounts of data useful for diagnostic and therapeutic developments. The lack of a simple and centralized way to exploit these data led us to design Yersiniomics, a web-based platform allowing straightforward analysis of Yersinia omics data. Yersiniomics contains a curated multi-omics database at its core, gathering 200 genomic, 317 transcriptomic, and 62 proteomic data sets for Yersinia species. It integrates genomic, transcriptomic, and proteomic browsers, a genome viewer, and a heatmap viewer to navigate within genomes and experimental conditions. For streamlined access to structural and functional properties, it directly links each gene to GenBank, the Kyoto Encyclopedia of Genes and Genomes (KEGG), UniProt, InterPro, IntAct, and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and each experiment to Gene Expression Omnibus (GEO), the European Nucleotide Archive (ENA), or the Proteomics Identifications Database (PRIDE). Yersiniomics provides a powerful tool for microbiologists to assist with investigations ranging from specific gene studies to systems biology studies. IMPORTANCE The expanding genus Yersinia is composed of multiple nonpathogenic species and a few pathogenic species, including the deadly etiologic agent of plague, Yersinia pestis. In 2 decades, the number of genomic, transcriptomic, and proteomic studies on Yersinia grew massively, delivering a wealth of data. We developed Yersiniomics, an interactive web-based platform, to centralize and analyze omics data sets on Yersinia species. The platform allows user-friendly navigation between genomic data, expression data, and experimental conditions. Yersiniomics will be a valuable tool to microbiologists.

Evaluation of a multi-species Protein A-ELISA assay for plague serologic diagnosis in humans and other mammal hosts

Background

The Hemagglutination assay (HA) is widely used in plague diagnosis, however, it has a subjective interpretation and demands high amounts of antigen and other immunobiological supplies. On the other hand, the conventional Anti-IgG ELISA is limited by the need of specific conjugates for multiple plague hosts, which leaves a gap for new diagnostic methods able to cover both the diagnosis of human cases and the epidemiological surveillance of multiple sentinel species.

Methods

We developed an ELISA Protein A-peroxidase method to detect anti-F1 antibodies across several species, including humans. To determine the cut-off and performance rates, HA results from 288 samples (81 rabbits, 64 humans, 66 rodents and 77 dogs) were used as reference. Next, we evaluated the agreement between Protein A-ELISA and Anti-IgG ELISA in an expanded sample set (n = 487).

Results

Optimal conditions were found with 250ng/well of F1 and 1:500 serum dilution. Protein A-ELISA showed high repeatability and reproducibility. We observed good correlation rates between the Protein A and IgG ELISAs optical densities and a higher positive/negative OD ratio for the Protein A-ELISA method. The overall sensitivity, specificity and area under the curve for Protein A-ELISA were 94%, 99% and 0.99, respectively. Similar results were observed for each species separately. In the analysis of the expanded sample set, there was a strong agreement between Protein A and IgG assays (kappa = 0.97). Furthermore, there was no cross-reaction with other common infectious diseases, such as dengue, Zika, Chagas disease, tuberculosis (humans) and ehrlichiosis, anaplasmosis and leishmaniasis (dogs).

Conclusions

Altogether, the Protein A-ELISA showed high performance when compared both to HA and Anti-IgG ELISA, with a polyvalent single protocol that requires reduced amounts of antigen and can be employed to any plague hosts.

Here, we developed and evaluated an ELISA diagnostic test based on the Protein A-peroxidase conjugate that allows the test to be used for plague laboratorial diagnosis not only in humans, but also in a wide range of mammalian species. This particularity is specifically important for plague epidemiological surveillance, given that Yersinia pestis, the causative agent of plague, have a long list of animal reservoirs across distinct ecosystems. Briefly, we first evaluated the best reaction parameters, such as antigen concentration, serum and protein A-conjugate dilutions. Next, we used serum samples from humans, dogs, rodents and rabbits (n = 288) with known results for plague serology by a conventional method, to evaluate the performance of the new Protein A-ELISA test. We observed a good performance of the novel Protein A-ELISA test, with high sensitivity and specificity rates. Evaluation of the coefficient of variation revealed that the test measurements suffer little variation, and therefore, has high repeatability and reproducibility. Next, by evaluating 487 samples, we observed a high degree of concordance between the Protein A-ELISA with a conventional IgG-based ELISA. Furthermore, this test showed no significant cross-reaction with other common infectious diseases. Altogether, the Protein A-ELISA showed high performance when compared both to HA and Anti-IgG ELISA, with a single protocol that requires reduced amounts of antigen and can be employed to several plague hosts.

Exploring and Mitigating Plague for One Health Purposes

Purpose of Review

In 2020, the Appropriations Committee for the U.S. House of Representatives directed the CDC to develop a national One Health framework to combat zoonotic diseases, including sylvatic plague, which is caused by the flea-borne bacterium Yersinia pestis. This review builds upon that multisectoral objective. We aim to increase awareness of Y. pestis and to highlight examples of plague mitigation for One Health purposes (i.e., to achieve optimal health outcomes for people, animals, plants, and their shared environment). We draw primarily upon examples from the USA, but also discuss research from Madagascar and Uganda where relevant, as Y. pestis has emerged as a zoonotic threat in those foci.

Recent Findings

Historically, the bulk of plague research has been directed at the disease in humans. This is not surprising, given that Y. pestis is a scourge of human history. Nevertheless, the ecology of Y. pestis is inextricably linked to other mammals and fleas under natural conditions. Accumulating evidence demonstrates Y. pestis is an unrelenting threat to multiple ecosystems, where the bacterium is capable of significantly reducing native species abundance and diversity while altering competitive and trophic relationships, food web connections, and nutrient cycles. In doing so, Y. pestis transforms ecosystems, causing "shifting baselines syndrome" in humans, where there is a gradual shift in the accepted norms for the condition of the natural environment. Eradication of Y. pestis in nature is difficult to impossible, but effective mitigation is achievable; we discuss flea vector control and One Health implications in this context.

Summary

There is an acute need to rapidly expand research on Y. pestis, across multiple host and flea species and varied ecosystems of the Western US and abroad, for human and environmental health purposes. The fate of many wildlife species hangs in the balance, and the implications for humans are profound in some regions. Collaborative multisectoral research is needed to define the scope of the problem in each epidemiological context and to identify, refine, and implement appropriate and effective mitigation practices.

Rodent management and cereal production in Asia: Balancing food security and conservation

Rodents present a major problem for food security in Asia where smallholder farming families are particularly vulnerable. We review here recent developments in the biology and management of rodent pests in cereal cropping systems in Asia. The past decade has seen a strong focus on ecologically-based rodent management (EBRM), its adoption in field studies significantly increased rice yields (6-15%) and income (>15%) in seven Asian countries. EBRM principles have also been successfully applied to maize in China. We provide case studies on EBRM in Cambodia, on interactions between rodent pests and weeds, and on the importance of modified wetlands for biodiversity and rodent pest management. Knowledge on post-harvest impacts of rodents is increasing. One research gap is the assessment of human health impacts from a reduction of rodent densities in and around houses. We identify 10 challenges for the next decade. For example, the need for population modelling, a valuable tool missing from our toolbox to manage rodent pests in cereal systems. We also need to understand better the interactive effects of cropping intensification, conservation agriculture and climate change. Finally, new management approaches such as fertility control are on the horizon and need to be considered in the context of smallholder cereal farming systems and mitigating health risks from zoonotic diseases associated with rodents. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Lessons Learnt From the COVID-19 Pandemic

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has been characterized by unprecedented rates of spatio-temporal spread. Here, we summarize the main events in the pandemic's timeline and evaluate what has been learnt by the public health community. We also discuss the implications for future public health policy and, specifically, the practice of epidemic control. We critically analyze this ongoing pandemic's timeline and contrast it with the 2002-2003 SARS outbreak. We identify specific areas (e.g., pathogen identification and initial reporting) wherein the international community learnt valuable lessons from the SARS outbreak. However, we also identify the key areas where international public health policy failed leading to the exponential spread of the pandemic. We outline a clear agenda for improved pandemic control in the future.

Transmission of antimicrobial resistant Yersinia pestis during a pneumonic plague outbreak

BACKGROUND

Pneumonic plague (PP), caused by Yersinia pestis, is the most feared clinical form of plague due to its rapid lethality and potential to cause outbreaks. PP outbreaks are now rare due to antimicrobial therapy.

METHODS

A PP outbreak in Madagascar involving transmission of a Y. pestis strain resistant to streptomycin, the current recommended first-line treatment in Madagascar, was retrospectively characterized using epidemiology, clinical diagnostics, molecular characterization, and animal studies.

RESULTS

The outbreak occurred in February 2013 in the Faratsiho district of Madagascar and involved 22 cases, including three untreated fatalities. The 19 other cases participated in funeral practices for the fatal cases and fully recovered after combination antimicrobial therapy: intramuscular streptomycin followed by oral co-trimoxazole. The Y. pestis strain that circulated during this outbreak is resistant to streptomycin resulting from a spontaneous point mutation in the 30S ribosomal protein S12 (rpsL) gene. This same mutation causes streptomycin resistance in two unrelated Y. pestis strains, one isolated from a fatal PP case in a different region of Madagascar in 1987 and another isolated from a fatal PP case in China in 1996, documenting this mutation has occurred independently at least three times in Y. pestis. Laboratory experiments revealed this mutation has no detectable impact on fitness or virulence, and revertants to wild-type are rare in other species containing it, suggesting Y. pestis strains containing it could persist in the environment.

CONCLUSION

Unique AMR strains of Y. pestis continue to arise in Madagascar and can be transmitted during PP outbreaks.

Efficacy of a combined insecticide-rodenticide product on ectoparasite and commensal rodent mortality

BACKGROUND

Ectoparasites may transfer zoonotic pathogens from rodents to humans or livestock when rodents are managed with rodenticides. This could be minimized using a product combining a rodenticide with a delayed action and a systemic insecticide/acaricide that rapidly kills ectoparasites. Such a combination was tested in commensal pest rodent species to assess efficacy and timing of responses in rodents, and fleas and ticks feeding on them. Ticks or fleas attached to rats (Rattus norvegicus) and house mice (Mus musculus domesticus) were exposed to a product containing brodifacoum (50 ppm) and fipronil (40 ppm) for three days.

RESULTS

98-100% of fleas on treated rodents died within one to two days after first exposure, whereas >90% fleas survived on control rodents. The effect persisted for four or more days after bait uptake. Ticks started to succumb to the effect of the combination product within one day (mice) and within four days (rats) of first exposure, with all ticks dying by Day (D)8. Tick survival in control rodents was 90-100%. Rodent mortality began at D3 (rats) and D4 (mice) after first consumption of product and all were dead by D9 (rats) and D7 (mice).

CONCLUSION

This product effectively killed ectoparasites and rodents. Flea mortality was swift and complete, generally within one day of exposure, whereas it took ticks up to four days to die, but before the rats and house mice died. The combination product might help to prevent ectoparasites migrating from dying rodents to another host. Field trials are warranted. © 2020 Society of Chemical Industry.

Past pandemics and climate variability across the Mediterranean

The influence that meteorological, climatological and environmental factors had on historical disease outbreaks is often speculated upon, but little investigated. Here, we explore potential associations between pandemic disease and climate over the last 2,500 years in Mediterranean history, focusing on ancient disease outbreaks and the Justinianic plague in particular. We underscore variation in the quality, quantity and interpretation of written evidence and proxy information from natural archives, the comlexity of identifying and disentangling past climatological and environmental drivers, and the need to integrate diverse methodologies to discern past climate-disease linkages and leverage historical experiences to prepare for the rapid expansion of novel pathogenic diseases. Although the difficulties entailed in establishing historical climate-pandemic linkages persist to the present, this is a research area as urgent as it is complex and historical perspectives are desperately needed.

Human plague: An old scourge that needs new answers

Yersinia pestis, the bacterial causative agent of plague, remains an important threat to human health. Plague is a rodent-borne disease that has historically shown an outstanding ability to colonize and persist across different species, habitats, and environments while provoking sporadic cases, outbreaks, and deadly global epidemics among humans. Between September and November 2017, an outbreak of urban pneumonic plague was declared in Madagascar, which refocused the attention of the scientific community on this ancient human scourge. Given recent trends and plague's resilience to control in the wild, its high fatality rate in humans without early treatment, and its capacity to disrupt social and healthcare systems, human plague should be considered as a neglected threat. A workshop was held in Paris in July 2018 to review current knowledge about plague and to identify the scientific research priorities to eradicate plague as a human threat. It was concluded that an urgent commitment is needed to develop and fund a strong research agenda aiming to fill the current knowledge gaps structured around 4 main axes: (i) an improved understanding of the ecological interactions among the reservoir, vector, pathogen, and environment; (ii) human and societal responses; (iii) improved diagnostic tools and case management; and (iv) vaccine development. These axes should be cross-cutting, translational, and focused on delivering context-specific strategies. Results of this research should feed a global control and prevention strategy within a "One Health" approach.

Specific Detection of Yersinia pestis Based on Receptor Binding Proteins of Phages

The highly pathogenic bacterium Yersinia pestis is the causative agent of plague, a notorious infectious zoonotic disease. When transmitted from person to person as pneumonic plague via droplets, Y. pestis is highly contagious and in most cases is fatal if left untreated. Thus, when plague is suspected, rapid diagnosis is crucial, as a serious course of the infection is only averted by early antibiotic therapy. The bacterium is easy to cultivate, accessible and has a high potential for nefarious use such as bioterrorism. Highly specific, rapid and easy-to-use confirmatory diagnostic methods are required to reliably identify the pathogen independently from PCR-based methods or F1 antigen-based immunological detection. Yersinia pestis specific phages such as L-413C and ΦA1122 are already used for detection of Y. pestis in bacterial plaque or biosensor assays. Here, we made use of the host specificities conferred by phage receptor binding (or tail fiber/spike) proteins (RBP) for developing a specific, fast and simple fluorescence-microscopy-based detection method for Y. pestis. Genes of putative RBP of phages L-413C (gpH) and ΦA1122 (gp17) were fused with those of fluorescent proteins and recombinant receptor-reporter fusion proteins were produced heterologously in Escherichia coli. When first tested on attenuated Y. pestis strain EV76, RBP-reporters bound to the bacterial cell surface. This assay could be completed within a few minutes using live or formaldehyde-inactivated cells. Specificity tests using cultures of closely related Yersinia species and several inactivated fully virulent Y. pestis strains exhibited high specificities of the RBP-reporters against Y. pestis. The L-413C RBP proved to be especially specific, as it only detected Y. pestis at all temperatures tested, whereas the RBP of ΦA1122 also bound to Y. pseudotuberculosis strains at 37 °C (but not at 28, 20 or 6 °C). Finally, the Y. pestis-specific capsule, produced when grown at 37 °C, significantly reduced binding of phage ΦA1122 RBP, whereas the capsule only slightly diminished binding of L-413C RBP.