Draft genome sequence of Yersinia pestis strain 2501, an isolate from the great gerbil plague focus in Xinjiang, China.

We deciphered the genome of Yersinia pestis strain 2501, isolated from the Junggar Basin, a newly discovered great gerbil plague focus in Xinjiang, China. The total length of assembly was 4,597,322 bp, and 4,265 coding sequences were predicted within the genome. It is the first Y. pestis genome from this plague focus.

Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment.

Yersinia pestis is transmitted from fleas to rodents when the bacterium develops an extensive biofilm in the foregut of a flea, starving it into a feeding frenzy, or, alternatively, during a brief period directly after feeding on a bacteremic host. These two transmission modes are in a trade-off regulated by the amount of biofilm produced by the bacterium. Here by investigating 446 global isolated Y. pestis genomes, including 78 newly sequenced isolates sampled over 40 years from a plague focus in China, we provide evidence for strong selection pressures on the RNA polymerase ω-subunit encoding gene rpoZ. We demonstrate that rpoZ variants have an increased rate of biofilm production in vitro, and that they evolve in the ecosystem during colder and drier periods. Our results support the notion that the bacterium is constantly adapting-through extended phenotype changes in the fleas-in response to climate-driven changes in the niche.

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

The 15th natural plague focus in China, the Junggar Basin plague focus, is located near an important communication route connecting China and Central Asia and was discovered after 2005. To characterize the phenotypic and genetic diversity of the Yersinia pestis population in this newly established focus, we collected 25 Y. pestis strains from six counties across Junggar Basin in 2005-2006, and determined their biochemical features and genotypes based on multiple-locus variable number of tandem repeats analysis and clustered regularly interspaced short palindromic repeats analysis. We inferred the phylogenetic positions and possible sources of the Junggar strains by comparing their genotypes with the genetic diversity for known representative Y. pestis strains. Our results indicate that the major genotype of Junggar strains belongs to 2.MED1, a lineage of biovar Medievalis with identical biochemical characters and high virulence in mice. Although share a similar ecology, the 2.MED1 in Junggar Basin are not descended from known strains in the neighboring Central Asian Desert plague foci. Therefore, the emergence of the Junggar Basin plague focus is not attributable to the recent clonal spread of Y. pestis from Central Asia. We also identified two distinct minor genotypes in Junggar Basin, one of which clusters genetically with the 0.ANT1 strains of the Tianshan Mountain natural plague focus and another belongs to a 1.IN lineage not previously reported. Our study clarifies the phenotypic and genetic characters of Junggar Y. pestis strains. These findings extend our knowledge of the population diversity of Y. pestis and will facilitate future plague surveillance and prevention in Junggar Basin and adjacent regions.

[Classification and diversity of tick community in Tarim basin].

OBJECTIVE: To investigate the distribution pattern and structural characteristics of tick community and to understand the diversity of the communities in Tarim Basin. METHODS: According to the geographical division and habitat types, survey sites were selected, and tick samples were collected and their species were identified. With the methods of community ecology, the richness, diversity and evenness of the tick community were calculated. The communities were classified by way of clustering analysis in combination with the environmental index of geology and vegetation. RESULTS: Totally 10 species belonging 5 genera of ticks were collected in the Basin. Hyalomma asiaticum asiaticum and Hyalomma asiaticum kozlovi were the dominant species in the area. The tick community was divided into 7 types in accordance with the environmental geology, vegetations, and their richness and coverage degree. CONCLUSIONS: There are abundant tick communities in the area of Tarim Basin, and a gradient change of the communities is continued in the ecological amplitude of this area.

Transmission efficiency of the plague pathogen (Y. pestis) by the flea, Xenopsylla skrjabini, to mice and great gerbils.

BACKGROUND: Plague, a zoonotic disease caused by Yersinia pestis, is characterized by its ability to persist in the plague natural foci. Junggar Basin plague focus was recently identified in China, with Rhombomys opimus (great gerbils) and Xenopsylla skrjabini as the main reservoir and vector for plague. No transmission efficiency data of X. skrjabini for Y. pestis is available till now. METHODS: In this study, we estimated the median infectious dose (ID50) and the blockage rates of X. skrjabini with Y. pestis, by using artificial feeders. We then evaluated the flea transmission ability of Y. pestis to the mice and great gerbils via artificial bloodmeal feeding. Finally, we investigated the transmission of Y. pestis to mice with fleas fed by infected great gerbils. RESULTS: ID50 of Y. pestis to X. skrjabini was estimated as 2.04 × 10(5) CFU (95% CI, 1.45 × 10(5) - 3.18 × 10(5) CFU), around 40 times higher than that of X. cheopis. Although fleas fed by higher bacteremia bloodmeal had higher infection rates for Y. pestis, they lived significantly shorter than their counterparts. X. skrjabini could get fully blocked as early as day 3 post of infection (7.1%, 3/42 fleas), and the overall blockage rate of X. cheopis was estimated as 14.9% (82/550 fleas) during the 14 days of investigation. For the fleas infected by artificial feeders, they seemed to transmit plague more efficiently to great gerbils than mice. Our single flea transmission experiments also revealed that, the transmission capacity of naturally infected fleas (fed by infected great gerbils) was significantly higher than that of artificially infected ones (fed by artificial feeders). CONCLUSION: Our results indicated that ID50 of Y. pestis to X. skrjabini was higher than other fleas like X. cheopis, and its transmission efficiency to mice might be lower than other flea vectors in the artificial feeding modes. We also found different transmission potentials in the artificially infected fleas and the naturally infected ones. Further studies are needed to figure out the role of X. skrjabini in the plague epidemiological cycles in Junggar Basin plague focus.

[Study on the spatial and temporal distribution of animal plague in Junggar Basin plague focus].

OBJECTIVE: To explore the spatial and temporal distributions of animal plague in Junggar Basin natural plague focus. METHODS: Data regarding plague antibody (F1) in serum of Great Gerbil (Rhombomys opimus, R. opimus) which were collected from 2005 to 2012 in Junggar Basin and analyzed. The changing rates on the positivity of F1 that appeared spatially and temporally were also analyzed. RESULTS: A total of 4 825 R. opimus serum samples were collected in 13 administrative regions in Junggar Basin. RESULTS: showed that plague R. opimus existed in two areas-Gurbantonggut desert in the eastern-center and the clay desert of western Junggar Basin. However, in these two areas, the intensity of animal plague prevalence was different. In the former region where Yesinia pestis positive serum was detected from R. opimus, the detected rate of R. opimus was 8.39%. However, in the latter areas, the average positive rate was 1.56%. The changing trends of R. opimus plague prevalence were also varied annually. In the western Junggar Basin, the trend showed a slowly downward profile. The serum positive rate of R. opimus for Yesinia pestis decreased, from 7.59% in 2005 to 0.61% in 2008, and appeared as a resting state that none of the positive sample could be found since then. However, in the eastern-center Junggar Basin area-also named as Gurbantonggut desert which had been divided into 3 segments(western, central and eastern, according to related geographical characteristics), the changing trends of animal plague seemed quite complex. In the western segment, the animal plague had two epidemic peaks-in 2006 and 2010, with the interval of 4 years, with the higher peak of all the three geographic segments as 45.65% in 2010 and the positive serum of R. opimus for plague could be detected each year from 2006 to 2012. However, there were 3 epidemic peaks in the same period in the central and eastern segments. In the central segment, the peaks appeared in 2006, 2009 and 2011, with the intervals as 2.5 years and the average positive rate 8.92% was seen the lowest in Gurbantonggut desert. In the eastern segment, the first 2 peaks appeared the same season as in the central segment, but the third peak appeared in 2012, with the peak interval as 3 years. The positive rate of R. opimus for plague was also different in seasons, with the positive rate higher in autumn than in spring. These findings showed that the animal plague could be continuously prevalent from spring to autumn in the natural foci of plague in the Junggar Basin. CONCLUSION: Both geographical and temporal fluctuations of animal plague existed in the natural foci of Junggar Basin which was also named as geographical heterogeneity. Consequently, animal plague could be divided into two areas-the clay plains desert in the western and the Gurbantonggut desert in the eastern-center Junggar Basin.

[Community structure of Great Gerbils (Rhombomys opimus) parasitic fleas in Junggar Basin focus and related epizootiological characteristics on plague].

OBJECTIVE: To understand the community structure of Rhombomys opimus parasitic fleas in the natural plague focus in Junggar Basin, so as to explain the relationship between the community structure and the prevalence of animal plague in this area. METHODS: The body fleas of R.opimus which were collected in 2005-2010 from the Junggar Basin was analysed by community ecology method, an each clustered flea community was compared with information of pathogenic and serological indicators of animal plague epidemic by statistic method. RESULTS: The community structure of R. opimus parasitic fleas included 19 species and was very complicated, with only 3 were identified as 'common' species but the others belonged to 'rare' species. Both the average richness and diversity of flea community were higher, as 1.66 and 1.5556, with dominance not obvious (0.332) and the homogeneity as moderate (0.5283). The community structure of R. opimus parasitic fleas could be changed by the following factors as: the rates of flea parasitic/flea index and the proportions of main fleas etc. The flea community could be divided into 5 clusters according to the above said elements. All these data showed that the fleas of R. opimus parasitic fleas possess the nature of multi-parasitism. CONCLUSIONS: The community of R. opimus parasitic fleas existed heterogeneous of geographic region, and this phenomenon associated with the animal plague epidemic strength.

Dynamics of Yersinia pestis and its antibody response in great gerbils (Rhombomys opimus) by subcutaneous infection.

BACKGROUND: Rhombomys opimus (great gerbil) is a reservoir of Yersinia pestis in the natural plague foci of Central Asia. Great gerbils are highly resistant to Y. pestis infection. The coevolution of great gerbils and Y. pestis is believed to play an important role in the plague epidemics in Central Asia plague foci. However, the dynamics of Y. pestis infection and the corresponding antibody response in great gerbils have not been evaluated. In this report, animal experiments were employed to investigate the bacterial load in both the liver and spleen of infected great gerbils. The dynamics of the antibody response to the F1 capsule antigen of Y. pestis was also determined. METHODOLOGY: Captured great gerbils that tested negative for both anti-F1 antibodies and bacterial isolation were infected subcutaneously with different doses (10(5) to 10(11) CFU) of a Y. pestis strain isolated from a live great gerbil during routine plague surveillance in the Junggar Basin, Xinjiang, China. The clinical manifestations, changes in body weight, anal temperature, and gross anatomy of the infected animals were observed. The blood cell count, bacterial load, and anti-F1 antibody titers were determined at different time points after infection using a blood analyzer, plate counts, and an indirect hemagglutination assay, respectively. CONCLUSIONS/SIGNIFICANCE: The dynamics of bacterial load and the anti-F1 antibody concentration in great gerbils are highly variable among individuals. The Y. pestis infection in great gerbils could persist as long as 15 days. They act as an appropriate reservoir for plague in the Junggar Basin, which is part of the natural plague foci in Central Asia. The dynamics of the Y. pestis susceptibility of great gerbil will improve the understanding of its variable resistance, which would facilitate the development of more effective countermeasures for controlling plague epidemics in this focus.

[Study on the situation of plague in Junggar Basin of China].

OBJECTIVE: To understand the distribution, fauna, population structure of host animals and their parasitic fleas as well as popular dynamic of animal plague of natural plague foci in Junggar Basin. METHODS: Sample materials and data of animals and vector insects were collected using ecological methods and the population structures were analyzed statistically. F1 antibody of Yersinia pestis in rodents' serum and organ suspension was detected by means of IHA while the pathogen of Y. pestis in rodents and vector insects was detected by means of aetiological detections and the isolated Y. pestis was detected using biochemical methods. RESULTS: The small mammals which were found in Junggar Basin belonged to 17 species of 11 genera 7 families. Of them, 13 species of rodents were included whose parasitic fleas belonged to 19 species of 10 genera 8 families. The average coverage of Rhombomys opimus hole-community was 22.5% in Junggar Basin with the average density of R. opimus hole-community was 15.9/hm2 and the average rate of habitat of the hole-community was 70.2%. In the R. opimus community, the average density of rodents was 3.1/hole-community, and 34.4/hm2 in the nature plague foci. In the population structure of the hole-community of R. opimus, R. opimus accounted for 72.9% in the total captured rodents, Meriones meridianus was 24.5% while the others were 2.6%. In the nocturnal community of rodents, M. meridianus accounted for 64.0% in total captured rodents, Dipus sagitta was 15.1%, M. erythrourns was 7.5% and the others were 13.4%. In the rodents community of Junggar Basin, the rate of R. opimus with fleas was 84.9%, which was the highest, followed by M. tamariscinus, Euchoreutes naso and M. erythrourns, with the rates as 71.4%, 66.7% and 62.7% respectively. The rate of M. meridianus with fleas was 38.3%. There were 16 species of parasitic fleas in R. opimus, with the total flea index as 8.58 and the dominant species was Xenopsylla skrjabini. There were 17 and 16 kinds of fleas in M. erythrourns and M. meridianus respectively with the total flea index were 1.59 and 1.15, with dominant fleas were Nosopsyllus laeviceps and X. skrjabini. The serum and organ suspension of 3179 rodents which belonged to 12 species were detected by means of IHA, of them 174 samples were positive and the positive rate was 5.5%. There were 1356 samples of R. opimus in these materials, and 164 were positive, accounted for 12.1%. The samples of M. meridianus were 1255, with 9 positive, accounted for 0.7%. The samples of D. sagitta were 116 with 1 positive and the rate was 0.9%. The samples of other rodents were 452 but were all negative. There were in total 2975 organs collected from rodents, when detected by methods of isolated of Y. pestis. 15 strains of Y. pestis were isolated from 1243 R. opimus, and 2 strains isolated from 1230 M. meridianus. A total number of 11 647 fleas from rodents were detected by methods of isolated of Y. pestis in which 1 strain of Y. pestis was isolated from 4713 X. skrjabini, and 6 were isolated from 2101 Xenopsylla minax, 1 from 328 Xenopsylla conformis conformis and 1 from 250 Echidnophaga oschanini. Among the other 4255 fleas, none was isolated. The biochemical properties of these Y. pestis which isolated from Junggar Basin were positive of Maltose, Ejiao sugar and Glycerol, and negative of Rhamnose and Nitrogen, which were all strongly poisonous to mouse. CONCLUSION: The natural plague foci in Junggar Basin spread all over the whole Junggar Basin. There were animal plague cases found in 12 counties (cites) while Karamy, Bole, Jimusaer and Qitai were confirmed as plague foci counties (cities). Animals and vector insects of the foci were complicated but the ecological system was stable. R. opimus was recognized as the dominant host animal and its biochemical type belonged to the Middle Ages, suggesting that the foci was a new type of natural plague foci.