Yan Y.,Beijing Institute of Microbiology and Epidemiology |
Wang H.,Qinghai Institute for Endemic Diseases Prevention and Control |
Li D.,BGI Shenzhen |
Yang X.,Beijing Institute of Microbiology and Epidemiology |
And 12 more authors.
PLoS ONE | Year: 2014
Source tracing of pathogens is critical for the control and prevention of infectious diseases. Genome sequencing by high throughput technologies is currently feasible and popular, leading to the burst of deciphered bacterial genome sequences. Utilizing the flooding genomic data for source tracing of pathogens in outbreaks is promising, and challenging as well. Here, we employed Yersinia pestis genomes from a plague outbreak at Xinghai county of China in 2009 as an example, to develop a simple two-step strategy for rapid source tracing of the outbreak. The first step was to define the phylogenetic position of the outbreak strains in a whole species tree, and the next step was to provide a detailed relationship across the outbreak strains and their suspected relatives. Through this strategy, we observed that the Xinghai plague outbreak was caused by Y. pestis that circulated in the local plague focus, where the majority of historical plague epidemics in the Qinghai-Tibet Plateau may originate from. The analytical strategy developed here will be of great help in fighting against the outbreaks of emerging infectious diseases, by pinpointing the source of pathogens rapidly with genomic epidemiological data and microbial forensics information. Copyright: © 2014 Yan et al.
Li Y.,Beijing Institute of Microbiology and Epidemiology |
Li Y.,Navy General Hospital |
Cui Y.,Beijing Institute of Microbiology and Epidemiology |
Cui B.,Qinghai Institute for Endemic Diseases Prevention and Control |
And 11 more authors.
PLoS ONE | Year: 2013
Background:Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.Methodology/Principal Findings:Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.Conclusions/Significance:Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis. © 2013 Li et al.
Zhao Z.-J.,Qinghai Institute for Endemic Diseases Prevention and Control
Chinese Journal of Endemiology | Year: 2010
Objective: To master the prevalence trend of Kaschin-Beck disease in Xinghai county (Shanglujuan and Xialujuan village of Tangnaihai township) from 2003 to 2008 in order to understand changes of selenium level of internal and external environments. Methods: According to monitoring method on national. Kaschin-Beck disease, we carried out epidemical investigation, clinical examination and X-ray photograph on school children aged 7 - 12 in Xinghai county, a monitoring region, and collected samples of hair and grain. The content of selenium was detected by 2,3-naphthalene fluorescence. Results: From 2003 to 2008, in Shanglujuan village, the prevalence rate of clinic examination was fluctuating between 0(0/34) - 17.14%(6/35); the detectable rate of X-ray examination was fluctuating between 11.11% (3/27) - 20.59% (7/34), the prevalence rates of metaphysis and extremities were fluctuating between 0(0/27) - 13.21%(7/53) and 2.63%(1/38) - 11.43%(4/35). In Xialujuan village, the prevalence rate of clinic examination was fluctuating between 2.94%(1/34) - 13.33% (6/45); the detectable rate of X-ray examination was fluctuating between 26.67%(12/45) - 43.63%(24/55), the prevalence rate of metaphysis and extremities were fluctuating between 8.33%(6/72) - 26.47%(9/34) and 13.33% (6/45) - 38.18%(21/55). The selenium contents in hair samples were (139.92 ±92.27), (134.98 ±63.77)μg/kg respectively in Shanglujuan and Xialujuan village in 2003; the selenium contents in grain samples were (12.90 ± 7.18), (14.58 ±9.90)μg/kg respectively in Shanglujuan and Xialujuan village in 2005. Conclusions: The prevalence state of Kaschin-Beck disease in national monitoring region is rigid and pathogenetic factors of Kaschin-Beck disease are active. Selenium levels of internal and external environments are low in this region.
Wang X.,Beijing Institute of Microbiology and Epidemiology |
Wang Z.,Qinghai Institute for Endemic Diseases Prevention and Control |
Guo Z.,Beijing Institute of Microbiology and Epidemiology |
Wei B.,Qinghai Institute for Endemic Diseases Prevention and Control |
And 5 more authors.
Clinical and Vaccine Immunology | Year: 2011
The serum levels of interleukin-2 (IL-2), gamma interferon (IFN-γ), tumor necrosis factor alpha (TNF-α), IL-4, IL-6, and IL-10 of pneumonic plague patients were determined by enzyme-linked immunosorbent assay. IL-6 was the only elevated cytokine in the patients, and its level increased with a clear time course, indicating that IL-6 might be a prognostic marker for predicting the progression of plague. Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Cui J.-H.,Chinese National Institute for Communicable Disease Control and Prevention |
Du X.-L.,Chinese National Institute for Communicable Disease Control and Prevention |
Wei R.-J.,Qinghai Institute for Endemic Diseases Prevention and Control |
Zhou H.-J.,Chinese National Institute for Communicable Disease Control and Prevention |
And 3 more authors.
Archives of Microbiology | Year: 2015
Multilocus sequence typing (MLST) has proven to be an effective approach for the subtyping isolates of the Cronobacter genus and to exhibit a high level of discrimination between isolates. In this study, 151 Cronobacter strains were isolated from different sources and provinces across China from 2010 to 2012 and analyzed by MLST. Their sequence type profiles were compared with strains from other countries which were widely geographically and temporally distributed. Out of 151 strains in this study, the majority of strains were Cronobacter sakazakii (70.9 %), C. malonaticus (15.9 %), C. dublinensis (10.6 %), C. turicensis (2.0 %), and C. muytjensii (0.7 %). The strains were divided into 85 sequence types (STs), among which only 17 had previously been reported in other countries. The 85 identified STs for the Cronobacter genus were grouped into 14 clonal complexes and 47 singletons according to eBURST algorithm. The Cronobacter isolated from China showed a high diversity when they were subtyped using the MLST method. When compared to the Cronobacter PubMLST database, some sequence types of strains cultured from food and/or water in this study were also the same with strains isolated from patients in other countries as reported previously. This result showed the potential hazard of strains contaminating water and weaning food from China. © 2015, Springer-Verlag Berlin Heidelberg.
Chen H.,Qinghai Institute for Endemic Diseases Prevention and Control |
Zhang Y.,Center for Disease Control and Prevention of the Xinjiang Uygur Autonomous Region |
Dai X.,Center for Disease Control and Prevention of the Xinjiang Uygur Autonomous Region |
Wang Q.,Center for Disease Control and Prevention of the Xinjiang Uygur Autonomous Region |
And 10 more authors.
Parasites and Vectors | Year: 2015
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 × 105 CFU (95% CI, 1.45 × 105 - 3.18 × 105 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. © 2015 Zhang et al.; licensee BioMed Central.
PubMed | Academy of Military Medical science Email, Qinghai Institute for Endemic Diseases Prevention and Control and Academy of Military Medical science
Type: Journal Article | Journal: Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi | Year: 2014
To type Yersinia (Y.) pestis isolates under different regions (DFR) and to observe their geographical distributions in China.23 DFRs primers and PMT1 (plasmid) primer were used to verify the DFR genomovars of Y. pestiss strains from 11 plague foci in China. A total of 3 044 Y. pestis isolates were involved for analysis on DFR profiles with the characteristics of geographical distribution.52 genomovars were verified in 3 044 Y. pestis strains in China in which 19 genomovars as major and 33 genomovars as minor genomovar. 21 new genomovars, namely genomovar 32 to genomovar 52 were described on the basis of 31 genomovars previously confirmed. Three new genomovars belonged to new major genomovars, namely Himalayan marmot natural plague foci of the Qinghai-Tibet plateau newly added genomovar 32 and genomovar 44 as major genomovars. Mongolian gerbil natural plague foci of Inner Mongolia plateau were newly added genomovar 50 as one of the major genomovars.Among 21 new genomovars, 3 were major genomovars, with Chinese Y. pestis DFR as the major genomovars which had obvious distribution characteristics.
PubMed | Qinghai Institute for Endemic Diseases Prevention and Control
Type: Journal Article | Journal: Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] | Year: 2014
To study the pathogenic ecology characteristics of plague in Qinghai plateau.Applied molecular biology techniques, conventional technologies and geographic information system (GIS) to study phenotypic traits, plasmid spectrum, genotype, infected host and media spectrum etc.of 952 Yersinia pestis strains in Qinghai plateau plague foci, which were separated from different host and media in different regions during 1954 to 2012.The ecotypes of these strains were Qingzang plateau (91.49%, 871/952),Qilian mountain (6.41%, 61/952) and Microtus fuscus (1.26%, 12/952).83.6% (796/952) of these strains contained all the 4 virulence factors (Fr1, Pesticin1,Virulence antigen, and Pigmentation), 93.26% (367/392) were velogenic strains confirmed by virulence test.725 Yersinia pestis strains were separated from Qinghai plateau plague foci carried 9 kinds of plasmid, among which 713 strains from Marmot himalayan plague foci carried 9 kinds of plasmid, the Mr were 610(6), 710(6), 2310(6), 2710(6), 3010(6), 4510(6), 5210(6), 6510(6) and 9210(6) respectively. 12 Yersinia pestis strains were separated from Microtus fuscus plague foci carried only 3 kinds of plasmid, the Mr were 610(6), 4510(6), 6510(6). Meanwhile, the strains carrying large plasmid (5210(6), 6510(6) and 9210(6)) were only distributed in particular geographical location, which had the category property. The research also confirmed that 841 Yersinia pestis strains from two kinds of plague foci in Qinghai plateau had 11 genomovars. The strains of Marmot himalayan plague foci were given priority to genomovar 5 and 8, amounted to 611 strains, genomovar 8 accounted for 56.00% (471/841), genomovar 5 accounted for 23.07% (194/841). Besides, 3 new genomovars, including new 1(62 strains), new 2(52 strains), new 3(48 strains) were newly founded, and 12 strains of Microtus fuscus plague foci were genomovar 14.The main host and media of Qinghai plateau plague foci directly affected the spatial distribution regularities of plague epidemic and the pathogens characteristics, meanwhile the polymorphism of plague ecological geographic landscape leds to the complexity of Yersinia pestis genotype.
PubMed | Qinghai Institute for Endemic Diseases Prevention and Control
Type: Journal Article | Journal: Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine] | Year: 2015
To analyze the plasmid features and geographical distribution characteristics of Yersinia pestis of different plague foci in China.A total of 2 213 Yersinia pestis strains were colected from 11 Chinese plague foci separated during 1943 to 2012, and plasmid DNA according to alkali cracking method, and measured the relative molecular mass (Mr) of plasmid DNA based on the standard plasmid contrast method, then analyzed the plasmid profiles by agar gel electrophoresis.A total of 2 213 strains had 16 kinds of plasmids with different Mr, including 410(6), 610(6), 710(6), 1310(6), 1610(6), 2010(6), 2210(6), 2310(6), 2710(6), 3010(6), 3610(6), 4510(6), 5210(6), 6510(6), 7210(6) and 9010(6). Plasmid were classified into 26 kinds of plasmid profiles. A total of 2 213 Yersinia pestis strains contained 4 large plasmids, 5210(6), 6510(6), 7210(6) and 9010(6), whose ratio was 22.10% (589/2 213), 75.60% (1 672/2 213), 0.17% (4/2 213), 2.12% (47/2 213), respectively. Among which, strains with plasmid 5210(6), 6510(6), 9010(6) distributed in Qinghai-Tibet plateau Himalayan Marmot natural plague foci, strains with 7210(6) plasmid only distributed in Inner Mongolia Meriones unguiculatus natural plague foci and Junggar Basin R. opimus natural plague foci, and 6510(6) plasmid distributed in all the other foci.Strains in Chinese 11 plague foci contained 4 kinds of large plasmid, the Mr respectively were 5210(6), 6510(6), 7210(6), 9010(6), which were classified into 26 kinds of plasmid profiles with other plasmid. These plasmid profiles distributed in relatively independent epidemic focus.
PubMed | Qinghai Institute for Endemic Diseases Prevention and Control
Type: Case Reports | Journal: Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | Year: 2011
Primary pneumonic plague (PPP) caused by Yersinia pestis is the most threatening clinical form of plague. An outbreak was reported in July 2009 in Qinghai Province, China.This outbreak was investigated by clinical, epidemiological, bacteriological, and immunological methods. Multilocus variable number tandem repeat analysis (MLVA) was used to track the source of the outbreak.The index case, a patient with PPP, contaminated 11 close contacts. All the 12 cases, including the index patient, experienced sudden onset of fever, headache, and productive coughing with bloody sputum. Three of them died. Nevertheless, another 61 direct and 256 indirect contacts were not infected during the 2-week quarantine. Antibodies to F1 antigen were detected in 9 survival cases, with a 4-fold increase in titers in serum samples collected at different periods. Seven strains of Y. pestis were isolated from dogs and patients. Field investigation and MLVA of the isolated strains revealed that this outbreak was started by a deceased dog.Dogs are believed to be an indicator animal for plague surveillance, but their association with PPP is rare. Our results provide evidence for this possibility, which suggests the public health significance of dogs as a source of plague.