Phenotypic and Molecular Genetic Characteristics of Yersinia pestis at an Emerging Natural Plague Focus, Junggar Basin, China

Genetic diversity of Rhombomys opimus and Meriones meridianus with potential divergence of plague resistance in the Junggar Basin plague focus based on RT1-Db1*exon1

In the Junggar Basin plague focus, Rhombomys opimus and Meriones meridianus live together, and their parasitic fleas have a similar community structure. However, R. opimus has significantly higher positive rates of Yersinia pestis and anti-F1 antibody compared with M. meridianus. In this study, Y. pestis- and antiF1 antibody-negative R. opimus and M. penicilliger were collected in Qitai county, Fukang city and Mulei county of the eastern part of the Junggar Basin. The genomic DNA was extracted from their spleen tissues, and RT1-Db1*exon1 was amplified through PCR procedure and then sequenced. Sequence analysis was performed and molecular diversity parameters were calculated and compared. The results showed that there were significant differences in nucleotide composition, amino acid composition, number and distribution of single nucleotide polymorphism (SNP) sites and number of haplotypes between R. opimus and M. penicilliger. The nucleotide diversity (π) for R. opimus was 0.00420 ± 0.00139, the haplotype diversity (h) was 0.833 ± 0.086, and the average number of nucleotide differences (K) was 2.02564. The π for M. penicilliger was 0.06569 ± 0.02524, and the h was 1.000 ± 0.045, and the K was 10.4444. The fixation index (FST) value between R. opimus and M. penicilliger was 0.9207. Furthermore, the FST value within R. opimus (0.0275) was significantly lower than that within M. penicilliger (0.2106), indicating a greater genetic variation of M. penicilliger compared with R. opimus. In conclusion, the genetic diversity analysis based on RT1-Db1*exon1 showed that M. penicilliger had higher gene polymorphism and greater genetic differentiation compared with R. opimus in the Junggar Basin plague focus, which might be associated with the low infection rate of Y. pestis.

Parallelism in Speciation and Intraspecific Diversification of the Plague Microbe Yersinia pestis

Modern "molecular genetic (MG) phylogenies" of the plague microbe Yersinia pestis, built on models of neutral evolution using statistical methods of phylogenetic analysis, contradict numerous obvious environmental (ECO) patterns and are not consistent with the concept of adaptatiogenesis. The reason for the discrepancy between MG and ECO phylogenies is seen in the underestimation by the MG approach of parallelisms in the processes of speciation and intraspecific diversification of the plague microbe. ECO methods showed the parallel tritope (almost) simultaneous speciation of three primary genovariants (populations, subspecies) Y. pestis 2.ANT3, 3.ANT2, and 4.ANT1 in three geographical populations of the Mongolian marmot (Marmota sibirica), which in the MG approach is mistaken for polytomy ("Big Bang"), caused by unknown natural phenomena on the eve of the first pandemic (Justinian's plague, 6th-8th centuries AD). The discrepancy between the MG and ECO interpretations of the evolution of intraspecifically-derived phylogenetic subbranches 0.PE and 2.MED is also associated with parallel evolutionary processes in independent lines, based on genovariants 2.ANT3, 3.ANT2, and 4.ANT1. The independence of these phylogenetic lines and parallelisms of sub-branches 0.PE and 2.MED associated with them are not taken into account in the MG approach. The prospect of creating a real phylogenetic tree for Y. pestis depends on a creative synthesis of the two approaches-MG and ECO.

Advanced Molecular-Genetic Methods and Prospects for Their Application for the Indication and Identification of <i>Yersinia pestis</i> Strains

The review provides an analysis of the literature data on the use of various modern molecular-genetic methods for the indication and identification of Yersinia pestis strains with different properties and degree of virulence, which is caused by the diverse natural conditions in which they circulate. The methods are also considered from the perspective of their promising application at three levels (territorial, regional and federal) of the system for laboratory diagnosis of infectious diseases at the premises of Rospotrebnadzor organizations to solve the problem of maintaining the sanitary and epidemiological well-being of the country’s population. The main groups of methods considered are as follows: based on the analysis of the lengths of restriction fragments (ribo- and IS-typing, pulse gel electrophoresis); based on the analysis of specific fragments (DFR typing, VNTR typing); based on sequencing (MLST, CRISPR analysis, SNP analysis); PCR methods (including IPCR, SPA); isothermal amplification methods (LAMP, HDA, RPA, SEA, PCA, SHERLOCK); DNA-microarray; methods using aptamer technology; bio- and nano-sensors; DNA origami; methods based on neural networks. We can conclude that the rapid development of molecular diagnostics and genetics is aimed at increasing efficiency, multi-factorial approaches and simplifying the application of techniques with no need for expensive equipment and highly qualified personnel for analysis. At all levels of the system for laboratory diagnosis of infectious diseases at the Rospotrebnadzor organizations, it is possible to use methods based on PCR, isothermal amplification, SHERLOCK, biosensors, and small-sized sequencing devices. At the territorial level, at plague control stations, the use of immuno-PCR and SPA for the indication of Y. pestis is viable. At the regional level, introduction of the technologies based on the use of aptamers and DNA chips looks promising. For the federal level, the use of DNA origami methods and new technologies of whole genome sequencing is a prospect within the framework of advanced identification, molecular typing and sequencing of the genomes of plague agent strains.

Yersinia pestis and Plague: some knowns and unknowns

Since its first identification in 1894 during the third pandemic in Hong Kong, there has been significant progress of understanding the lifestyle of Yersinia pestis, the pathogen that is responsible for plague. Although we now have some understanding of the pathogen's physiology, genetics, genomics, evolution, gene regulation, pathogenesis and immunity, there are many unknown aspects of the pathogen and its disease development. Here, we focus on some of the knowns and unknowns relating to Y. pestis and plague. We notably focus on some key Y. pestis physiological and virulence traits that are important for its mammal-flea-mammal life cycle but also its emergence from the enteropathogen Yersinia pseudotuberculosis. Some aspects of the genetic diversity of Y. pestis, the distribution and ecology of plague as well as the medical countermeasures to protect our population are also provided. Lastly, we present some biosafety and biosecurity information related to Y. pestis and plague.

Polygenic plague resistance in the great gerbil uncovered by population sequencing

Pathogens can elicit high selective pressure on hosts, potentially altering genetic diversity over short evolutionary timescales. Intraspecific variation in immune response is observable as variable survivability from specific infections. The great gerbil (Rhombomys opimus) is a rodent plague host with a heterogenic but highly resistant phenotype. Here, we investigate the genomic basis for plague-resistant phenotypes by exposing wild-caught great gerbils to plague (Yersinia pestis). Whole genome sequencing of 10 survivors and 10 moribund individuals revealed a subset of genomic regions showing elevated differentiation. Gene ontology analysis of candidate genes in these regions demonstrated enrichment of genes directly involved in immune functions, cellular metabolism and the regulation of apoptosis as well as pathways involved in transcription, translation, and gene regulation. Transcriptomic analysis revealed that the early activated great gerbil immune response to plague consisted of classical components of the innate immune system. Our approach combining challenge experiments with transcriptomics and population level sequencing, provides new insight into the genetic background of plague-resistance and confirms its complex nature, most likely involving multiple genes and pathways of both the immune system and regulation of basic cellular functions.

Flea index predicts plague epizootics among great gerbils (Rhombomys opimus) in the Junggar Basin China plague focus

Background

The Junggar Basin plague focus was the most recently identified natural plague focus in China. Through extensive field investigations, great gerbils (Rhombomys opimus) have been confirmed as the main host in this focus, and the community structure of their parasitic fleas is associated with the intensity of plague epizootics. The aim of this study is to provide an indicator that can be surveyed to evaluate the risk of plague epizootics.

Methods

Between 2005 and 2016, rodents and fleas were collected in the Junggar Basin plague focus. The parasitic fleas on great gerbils were harvested, and anti-F1 antibody in the serum or heart infusion of great gerbils was detected through indirect hemagglutination assay. Yersinia pestis (Y. pestis) was isolated from the liver and spleen of great gerbils and their parasitic fleas using Luria-Bertani plates. Receiver-operating characteristic (ROC) curve was used to evaluate the predictive value of flea index.

Results

Between 2005 and 2016, 98 investigations were performed, and 6778 great gerbils and 68,498 fleas were collected. Twenty-seven rodents were positive for Y. pestis isolation with a positivity rate of 0.4%; 674 rodents were positive for anti-F1 antibody with a positivity rate of 9.9%. Among these 98 investigations, plague epizootics were confirmed in 13 instances by Y. pestis-positive rodents and in 59 instances by anti-F1 antibody-positive rodents. We observed a higher flea index among rodents with confirmed plague epizootic compared to the negative ones (P = 0.001, 0.002), with an AUC value of 0.659 (95% CI: 0.524–0.835, P = 0.038) for Y. pestis-positive rodents and an AUC value of 0.718 (95% CI: 0.687–0.784, P < 0.001) for anti-F1 antibody-positive rodents.

Conclusions

Significantly higher flea index was associated with confirmed plague epizootic cases among great gerbils and could be used to predict plague epizootics in this focus.

Graphical Abstract

New Genotype of Yersinia pestis Found in Live Rodents in Yunnan Province, China

Yunnan Province, China is thought to be the original source of biovar Orientalis of Yersinia pestis, the causative agent of the third plague pandemic that has spread globally since the end of the 19th century. Although encompassing a large area of natural plague foci, Y. pestis strains have rarely been found in live rodents during surveillance in Yunnan, and most isolates are from rodent corpses and their fleas. In 2017, 10 Y. pestis strains were isolated from seven live rodents and three fleas in Heqing County of Yunnan. These strains were supposed to have low virulence to local rodents Eothenomys miletus and Apodemus chevrieri because the rodents were healthy and no dead animals were found in surrounding areas, as had occurred in previous epizootic disease. We performed microscopic and biochemical examinations of the isolates, and compared their whole-genome sequences and transcriptome with those of 10 high virulence Y. pestis strains that were isolated from nine rodents and one parasitic flea in adjacent city (Lijiang). We analyzed the phenotypic, genomic, and transcriptomic characteristics of live rodent isolates. The isolates formed a previously undefined monophyletic branch of Y. pestis that was named 1.IN5. Six SNPs, two indels, and one copy number variation were detected between live rodent isolates and the high virulence neighbors. No obvious functional consequence of these variations was found according to the known annotation information. Among genes which expression differential in the live rodent isolates compared to their high virulent neighbors, we found five iron transfer related ones that were significant up-regulated (| log₂ (FC) | > 1, p.adjust < 0.05), indicating these genes may be related to the low-virulence phenotype. The novel genotype of Y. pestis reported here provides further insights into the evolution and spread of plague as well as clues that may help to decipher the virulence mechanism of this notorious pathogen.

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.

Soil salinity and aridity specify plague foci in the United States of America

Plague is a deadly zoonosis that periodically reemerges as small outbreaks in geographically limited foci where the causative agent Yersinia pestis may reside in soil. We analyzed a dataset of 1.005 carefully documented plague cases that were georeferenced over 113 years in peer-reviewed literature in the contiguous United States. Plotting outbreaks by counties defined as plague foci on geographical maps, we observed a significant co-localization of plague outbreaks with high soil salinity measured by an electric conductivity of >4 dS/ m^-1 and aridity measured by an aridity index <0.5. Thus, we identified aridity and soil salinity as significantly associated with ecological risk factors for relapsing plague in the contiguous United States. These results reveal two evolutive parameters that are partially associated with anthropic activities, complicating the epidemiology of plague in the contiguous United States. Exploiting aridity and soil salinity data may help in the surveillance of evolving plague foci in the contiguous United States.