DNA microarray analysis of genome dynamics in Yersinia pestis: insights into bacterial genome microevolution and niche adaptation

Genomics research provides an unprecedented opportunity for us to probe into the pathogenicity and evolution of the world's most deadly pathogenic bacterium, Yersinia pestis, in minute detail. In our present work, extensive microarray analysis in conjunction with PCR validation revealed that there are considerable genome dynamics, due to gene acquisition and loss, in natural populations of Y. pestis. We established a genomotyping system to group homologous isolates of Y. pestis, based on profiling or gene acquisition and loss in their genomes, and then drew an outline of parallel microevolution of the Y. pestis genome. The acquisition of a number of genomic islands and plasmids most likely induced Y. pestis to evolve rapidly from Yersinia pseudotuberculosis to a new, deadly pathogen. Horizontal gene acquisition also plays a key role in the dramatic evolutionary segregation of Y. pestis lineages (biovars and genomovars). In contrast to selective genome expansion by gene acquisition, genome reduction occurs in Y. pestis through the loss of DNA regions. We also theorized about the links between niche adaptation and genome microevolution. The transmission, colonization, and expansion of Y. pestis in the natural foci of endemic plague are parallel and directional and involve gradual adaptation to the complex of interactions between the environment, the hosts, and the pathogen itself. These adaptations are based on the natural selections against the accumulation of genetic changes within genome. Our data strongly support that the modern plague originated from Yunnan Province in China, due to the arising of biovar orientalis from biovar antiqua rather than mediaevalis.     

A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus

Yersinia pestis, the plague bacillus, has an exceptional pathogenicity but the factors responsible for its extreme virulence are still unknown. A genome comparison with its less virulent ancestor Yersinia pseudotuberculosis identified a few Y. pestis-specific regions acquired after their divergence. One of them potentially encodes a prophage (YpfPhi), similar to filamentous phages associated with virulence in other pathogens. We show here that YpfPhi forms filamentous phage particles infectious for other Y. pestis isolates. Although it was previously suggested that YpfPhi is restricted to the Orientalis branch, our results indicate that it was acquired by the Y. pestis ancestor. In Antiqua and Medievalis strains, YpfPhi genome forms an unstable episome whereas in Orientalis isolates it is stably integrated as tandem repeats. Deletion of the YpfPhi genome does not affect Y. pestis ability to colonize and block the flea proventriculus, but results in an alteration of Y. pestis pathogenicity in mice. Our results show that transformation of Y. pestis from a classical enteropathogen to the highly virulent plague bacillus was accompanied by the acquisition of an unstable filamentous phage. Continued maintenance of YpfPhi despite its high in vitro instability suggests that it confers selective advantages to Y. pestis under natural conditions.     

Flea diversity as an element for persistence of plague bacteria in an East African plague focus

Plague is a flea-borne rodent-associated zoonotic disease that is caused by Yersinia pestis and characterized by long quiescent periods punctuated by rapidly spreading epidemics and epizootics. How plague bacteria persist during inter-epizootic periods is poorly understood, yet is important for predicting when and where epizootics are likely to occur and for designing interventions aimed at local elimination of the pathogen. Existing hypotheses of how Y. pestis is maintained within plague foci typically center on host abundance or diversity, but little attention has been paid to the importance of flea diversity in enzootic maintenance. Our study compares host and flea abundance and diversity along an elevation gradient that spans from low elevation sites outside of a plague focus in the West Nile region of Uganda (~725-1160 m) to higher elevation sites within the focus (~1380-1630 m). Based on a year of sampling, we showed that host abundance and diversity, as well as total flea abundance on hosts was similar between sites inside compared with outside the plague focus. By contrast, flea diversity was significantly higher inside the focus than outside. Our study highlights the importance of considering flea diversity in models of Y. pestis persistence.     

The rodent. Akodon arviculoides, Wagner, 1842 (Cricetidae)--importance in plague foci in Brazil

The occurrence of the rodent Akodon arviculoides Wagner, 1842 in the plague focus of the "Agreste" region of the State of Pernambuco and a report on its ability for survival, reproduction and development in captivity, its susceptibility to Yersinia pestis infection and the role of this rodent species in Brazilian plague foci are reported.     

Dispersal of the flea Ctenophyllus hirticrus and spreading of plague epizooties in Gorny Altai

Gradual dispersion of an abundant flea species Ctenophyllus hirticrus specific to the Pallas's pika (the main plague carrier), is revealed in the Gorno-Altai natural plague focus on the territory, occupied by two populations of this lagomorph. Spreading of Yersinia pestis in these areas took place a short time later the rise of this ectoparasite's abundance. It is supposed that the colonization of these areas by C. hirticrus was one of the factors determined epizooties spreading within the focus and formation of new sites of stable Y. pestis preservation.     

Comparative genomics of 2009 seasonal plague (Yersinia pestis) in New Mexico

Plague disease caused by the gram-negative bacterium Yersinia pestis routinely affects animals and occasionally humans, in the western United States. The strains native to the North American continent are thought to be derived from a single introduction in the late 19(th) century. The degree to which these isolates have diverged genetically since their introduction is not clear, and new genomic markers to assay the diversity of North American plague are highly desired. To assay genetic diversity of plague isolates within confined geographic areas, draft genome sequences were generated by 454 pyrosequencing from nine environmental and clinical plague isolates. In silico assemblies of Variable Number Tandem Repeat (VNTR) loci were compared to laboratory-generated profiles for seven markers. High-confidence SNPs and small Insertion/Deletions (Indels) were compared to previously sequenced Y. pestis isolates. The resulting panel of mutations allowed clustering of the strains and tracing of the most likely evolutionary trajectory of the plague strains. The sequences also allowed the identification of new putative SNPs that differentiate the 2009 isolates from previously sequenced plague strains and from each other. In addition, new insertion points for the abundant insertion sequences (IS) of Y. pestis are present that allow additional discrimination of strains; several of these new insertions potentially inactivate genes implicated in virulence. These sequences enable whole-genome phylogenetic analysis and allow the unbiased comparison of closely related isolates of a genetically monomorphic pathogen.     

No evidence of persistent Yersina pestis infection at prairie dog colonies in north-central Montana

Sylvatic plague is a flea-borne zoonotic disease caused by the bacterium Yersinia pestis, which can cause extensive mortality among prairie dogs (Cynomys) in western North America. It is unclear whether the plague organism persists locally among resistant host species or elsewhere following epizootics. From June to August 2002 and 2003 we collected blood and flea samples from small mammals at prairie dog colonies with a history of plague, at prairie dog colonies with no history of plague, and from off-colony sites where plague history was unknown. Blood was screened for antibody to Y. pestis by means of enzyme-linked immunosorbent assay or passive hemagglutination assay and fleas were screened for Y. pestis DNA by polymerase chain reaction. All material was negative for Y. pestis including 156 blood samples and 553 fleas from colonies with a known history of plague. This and other studies provide evidence that Y. pestis may not persist at prairie dog colonies following an epizootic.     

Comparative and evolutionary genomics of Yersinia pestis

Yersinia pestis is the causative agent of plague, causing three human plague pandemics in history. Comparative and evolutionary genomics of Y. pestis are extensively discussed in this review. Understanding the genomic variability and the adaptive evolution of Y. pestis from the genomic point of view will contribute greatly to plague detection, identification, control and prevention.     

Epizootological role of fleas in the Gorno-Altai natural plague focus (a review)

Epizootological role of fleas in the Gorno-Altai natural plague focus (Sailugemsk focus) and numerous data on the flea viability are analyzed and generalized. Information concerning the flea natural infectivity with Yersinia pestis altaica is represented. Ecological peculiarities of some flea species parasitizing the main host, Mongolian pika Ochotona pallasi, and nature of their interrelations with Y. pestis are investigated. It is shown that the flea taxocenosis provides the permanent all year-round circulation of Y. pestis in the Gorno-Altai natural focus. Certain combinations of structural elements of the flea taxocenosis have a dominant significance in determination the circulation process at different phases of the annual epizootic cycle.     

Prevalence of Yersinia pestis in rodents and fleas associated with black-tailed prairie dogs (Cynomys ludovicianus) at Thunder Basin National Grassland, Wyoming

Rodents (and their fleas) that are associated with prairie dogs are considered important for the maintenance and transmission of the bacterium (Yersinia pestis) that causes plague. Our goal was to identify rodent and flea species that were potentially involved in a plague epizootic in black-tailed prairie dogs at Thunder Basin National Grassland. We collected blood samples and ectoparasites from rodents trapped at off- and on-colony grids at Thunder Basin National Grassland between 2002 and 2004. Blood samples were tested for antibodies to Y. pestis F-1 antigen by a passive hemagglutination assay, and fleas were tested by a multiplex polymerase chain reaction, for the presence of the plague bacterium. Only one of 1,421 fleas, an Oropsylla hirsuta collected in 2002 from a deer mouse, Peromyscus maniculatus, tested positive for Y. pestis. Blood samples collected in summer 2004 from two northern grasshopper mice, Onychomys leucogaster, tested positive for Y. pestis antibodies. All three positive samples were collected from on-colony grids shortly after a plague epizootic occurred. This study confirms that plague is difficult to detect in rodents and fleas associated with prairie dog colonies, unless samples are collected immediately after a prairie dog die-off.     

Yersinia pestis factors,assuring circulation and maintenance of the plague pathogen in natural foci ecosystems. Report 1

Everlasting reproduction of Yersinia pestis, plague bacillus in natural pestholes needs virulent causative agent to invade into the host entity, be potent to overcome protection powers of the rodent organism and to pullulate to entail bacteriemia for subsequent conveyance the plague bacillus to the new host by fleas. All of legs of life cyclic patterns of Yersinia pestis are maintained by a number of plague bacillus factors acting jointly or separately, participating at the different stages of infectious process or conveyance. However these factors provide the perpetuation of the plague bacillus in the ecosystems of natural pestholes only acting in conjunction independently on their distinct contributions. Not only biomolecules, organellas and bacteria systems ensured the pursuance of virulent properties, but other factors, essential for survival of Yersinia pestis and the relationship between separate virulence factors and expression of the different genes of housekeeping and virulence of plague bacillus are considered in this review. The report I covers the problems concerned with adaptational plasticity of Yersinia pestis, it represents the classification of plague causative factors, securing its perpetuation in the environmental space, and discussion the factors promoting plague bacillus survival in the host entity. Not only wellknown publications, but papers in out-of-the-way or hard-to-reach, especially for English-reading experts, editions, also were used to compile this communication. The English version of this review may be requested from Alerton Press.     

Susceptibility to Yersinia pestis in the northern grasshopper mouse (Onychomys leucogaster)

The laboratory-born progeny from two geographically distant populations of northern grasshopper mice (Onychomys leucogaster) were challenged with Yersinia pestis to determine their relative susceptibilities to plague. One of the O. leucogaster populations was associated with a known epizootic focus of the disease and was found to be nearly 2,000 times more resistant to mortality than were members of another population from an area historically free of plague. The ecology and omnivorous behavior of O. leucogaster appears to promote strong selection for resistance to plague in areas where they are naturally exposed.     

Changes in the activity of oxygen-dependent metabolism in polymorphonuclear leukocytes and macrophages from a primary focus during experimental Y. pestis infection in the mouse

The activity of oxygen-dependent metabolism (OM) was investigated in phagocytosing cells from a primary focus in plague infection using a mouse model. Experimental animals were given various i.p. doses of a virulent culture of Y. pestis. Changes in the OM of neutrophils and macrophages derived from peritoneal exudate after Y. pestis administration were phased and identical to non-specific post-aggression fluctuating reaction (PFR) comprising: 1. immediate depression phase, 2. overexertion phase and 3. exhaustion phase.     

Experimentally induced plague infection in the northern grasshopper mouse (Onychomys leucogaster) acquired by consumption of infected prey

In this study, 20 laboratory reared Onychomys leucogaster from a parental population that is naturally exposed to plague were each fed a white mouse that had been inoculated with Yersinia pestis. Three of the 20 O. leucogaster died, four survived with antibody titers against Y. pestis and 13 survived with no titer against Y. pestis. In contrast, when 20 O. leucogaster from a plague naive parental population were fed infected prey, seven died and 13 survived with no antibody titer against Y. pestis. Our results suggest another means by which O. leucogaster from populations that are naturally exposed to plague may acquire the disease.     

环介导等温扩增技术检测鼠疫耶尔森菌的敏感性和特异性研究

为观察环介导等温扩增(loop-mediated isothermal amplification,LAMP)技术能否适用于我国不同疫源地鼠疫耶尔森菌所有基因组型的检测,本研究建立了一种基于3a靶序列设计特异性引物快速检测鼠疫耶尔森菌的LAMP方法.选择分离自我国11个鼠疫自然疫源地的65株野生代表性鼠疫耶尔森菌株,同...     

鼠疫的发病机制研究进展

鼠疫是由鼠疫耶尔森菌(Yersinia pestis，Y. pestis)感染引起的一种人畜共患病。鼠疫在世界范围内出现过3次大流行，均引起致命的瘟疫。由于自然疫源面积不断扩大和人口流动愈加频繁，我国的鼠疫防治形势依旧严峻。本文就鼠疫耶尔森菌的毒力因子、对宿主细胞的黏附和侵袭、胞内繁殖、宿主内播散等机制的研究进展进行总结，有助于揭示鼠疫独特的致病和传播机制，为精准防治鼠疫提供工作基础。     

Bacteriologic and serologic studies of an outbreak of plague in the State of Paraíba, Brazil

During a plaque outbreak in the Borborema Plateau focus (Paraiba), bacteriological and serological studies were carried out in material from 452 patients (48 positives), 1,938 rodents and other small mammals (75 positives), 4,756 dogs (141 positives) and 2,047 cats (57 positives) obtained from 41 counties (out of which, 21 produced positive samples). Twenty Yersinia pestis strains isolated from material from 3 patients and 17 rodents, displayed biochemical reactions, virulence factors, antibiotic susceptibility and animal experimental pathogenicity similar to those observed in strains previously isolated. According to our findings this recent plague outbreak did not exhibit different factors from those observed during prior outbreaks in other plague foci in the northeast of Brazil.     

Identification and characterization of autotransporter proteins of Yersinia pestis KIM

Yersinia pestis is a Gram-negative bacterium that causes plague. Currently, plague is considered a re-emerging infectious disease and Y. pestis a potential bioterrorism agent. Autotransporters (ATs) are virulence proteins translocated by a variety of pathogenic Gram-negative bacteria across the cell envelope to the cell surface or extracellular environment. In this study, we screened the genome of Yersinia pestis KIM for AT genes whose expression might be relevant for the pathogenicity of this plague-causing organism. By in silico analyses, we identified ten putative AT genes in the genomic sequence of Y. pestis KIM; two of these genes are located within known pathogenicity islands. The expression of all ten putative AT genes in Y. pestis KIM was confirmed by RT-PCR. Five genes, designated yapA, yapC, yapG, yapK and yapN, were subsequently cloned and expressed in Escherichia coli K12 for protein secretion studies. Two forms of the YapA protein (130 kDa and 115 kDa) were found secreted into the culture medium. Protease cleavage at the C terminus of YapA released the protein from the cell surface. Outer membrane localization of YapC (65 kDa), YapG (100 kDa), YapK (130 kDa), and YapN (60 kDa) was established by cell fractionation, and cell surface localization of YapC and YapN was demonstrated by protease accessibility experiments. In functional studies, YapN and YapK showed hemagglutination activity and YapC exhibited autoagglutination activity. Data reported here represent the first study on Y. pestis ATs.     

Yersinia pestis and plague: an updated view on evolution,virulence determinants,immune subversion,vaccination and diagnostics

Plague is a vector-borne disease caused by Yersinia pestis. Transmitted by fleas from rodent reservoirs, Y. pestis emerged less than 6000 years ago from an enteric bacterial ancestor through events of gene gain and genome reduction. It is a highly remarkable model for the understanding of pathogenic bacteria evolution, and a major concern for public health as highlighted by recent human outbreaks. A complex set of virulence determinants, including the Yersinia outer membrane proteins (Yops), the broad range protease Pla, pathogen-associated molecular patterns (PAMPs) and iron capture systems play critical roles in the molecular strategies that Y. pestis employs to subvert the human immune system, allowing unrestricted bacterial replication in lymph nodes (bubonic plague) and in lungs (pneumonic plague). Some of these immunogenic proteins as well as the capsular antigen F1 are exploited for diagnostic purposes, which are critical in the context of the rapid onset of death in the absence of antibiotic treatment (less than a week for bubonic plague and less than 48 h for pneumonic plague). In here, we review recent research advances on Y. pestis evolution, virulence factors function, bacterial strategies to subvert mammalian innate immune responses, vaccination and problems associated to pneumonic plague diagnosis.     

Role of the Yersinia pestis yersiniabactin iron acquisition system in the incidence of flea-borne plague

Plague is a flea-borne zoonosis caused by the bacterium Yersinia pestis. Y. pestis mutants lacking the yersiniabactin (Ybt) siderophore-based iron transport system are avirulent when inoculated intradermally but fully virulent when inoculated intravenously in mice. Presumably, Ybt is required to provide sufficient iron at the peripheral injection site, suggesting that Ybt would be an essential virulence factor for flea-borne plague. Here, using a flea-to-mouse transmission model, we show that a Y. pestis strain lacking the Ybt system causes fatal plague at low incidence when transmitted by fleas. Bacteriology and histology analyses revealed that a Ybt-negative strain caused only primary septicemic plague and atypical bubonic plague instead of the typical bubonic form of disease. The results provide new evidence that primary septicemic plague is a distinct clinical entity and suggest that unusual forms of plague may be caused by atypical Y. pestis strains.