Clade 2.3.2.1 #H5N1 #avian #influenza viruses circulate at the interface of #migratory and domestic #birds around #Qinghai Lake in #China (Vet Microbiol., abstract)

[Source: US National Library of Medicine, full page: (LINK). Abstract, edited.]

Vet Microbiol. 2019 Aug;235:234-242. doi: 10.1016/j.vetmic.2019.07.009. Epub 2019 Jul 11.

Clade 2.3.2.1 H5N1 avian influenza viruses circulate at the interface of migratory and domestic birds around Qinghai Lake in China.

Yang J1, Wang Z1, Du Y1, Jia Y1, Wang L1, Xu S2, Zhu Q3.

Author information: 1 State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Lanzhou 730046, China. 2 State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Lanzhou 730046, China. Electronic address: xushuai@caas.cn. 3 State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Lanzhou 730046, China. Electronic address: zhuqiyun@caas.cn.

 

Abstract

During 2012-2015, six H5N1 avian influenza viruses were isolated from domestic birds and the environment around Qinghai Lake. Phylogenetic analysis of HA genes revealed that A/chicken/Gansu/XG2/2012 (CK/GS/XG2/12) belonged to clade 2.3.2.1a, while A/environment/Qinghai/1/2013 (EN/QH/1/13), A/chicken/Qinghai/QH1/2015 (CK/QH/QH1/15), A/chicken/Qinghai/QH2/2015 (CK/QH/QH2/15), A/chicken/Qinghai/QH3/2015 (CK/QH/QH3/15), and A/goose/Qinghai/QH6/2015 (GS/QH/QH6/15) belonged to clade 2.3.2.1c. Further analysis of the internal genes of the isolates found that the PB2 gene of EN/QH/1/13 had 99.6% nucleotide identity with that of A/tiger/Jiangsu/1/2013 (H5N1), which clustered into an independent branch with PB2 from multiple subtypes. PB2, PB1, and M genes of CK/QH/QH3/15 were from H9N2, suggesting it was a reassortant of H5N1 and H9N2. Animal studies of three selected viruses revealed that CK/GS/XG2/12, EN/QH/1/13, and CK/QH/QH3/15 were highly lethal to chickens, with intravenous pathogenicity indexes (IVPIs) of 2.97, 2.81, and 3.00, respectively, and systemically replicated in chickens. In a mouse study, three selected H5N1 viruses were highly pathogenic to mice and readily replicated in the lungs, nasal turbinates, kidneys, spleens, and brains. Therefore, isolates in this study appear to be novel reassortants that were circulating at the interface of wild and domestic birds around Qinghai Lake and are lethal to chickens and mice. These data suggest that more extensive surveillance should be implemented, and matched vaccines should be chosen for the domestic birds in this area.

Copyright © 2019 Elsevier B.V. All rights reserved.

KEYWORDS: H5N1; Interface; Migratory or domestic bird; Qinghai Lake; Virus evolution

PMID: 31383307 DOI: 10.1016/j.vetmic.2019.07.009

Keywords: Avian Influenza; H5N1; H9N2; Reassortant strain; Poultry; Wild Birds; Animal Models; China.

——-

Advertisements

High #colonization rate of a novel #carbapenem-resistant #Klebsiella lineage among #migratory #birds at #Qinghai Lake, #China (J Antimicrob Chemother., abstract)

[Source: Journal of Antimicrobial Chemotherapy, full page: (LINK). Abstract, edited.]

High colonization rate of a novel carbapenem-resistant Klebsiella lineage among migratory birds at Qinghai Lake, China

Xiaoping Liao, Run-Shi Yang, Jing Xia, Liang Chen, Rongmin Zhang, Liang-Xing Fang,Fumin Lei, Gang Song, Ling Jia, Lu Han, Shuancheng Bai, Rina Bai, Jian Sun,Ya-Hong Liu

Journal of Antimicrobial Chemotherapy, dkz268, https://doi.org/10.1093/jac/dkz268

Published: 24 July 2019

 

Abstract

Objectives

The emergence of carbapenemase-positive Enterobacteriaceae poses a serious threat to public health worldwide. Here we conducted a molecular surveillance study on carbapenem-resistant Enterobacteriaceae (CRE) colonization among migratory birds at Qinghai Lake in China.

Methods

A total of 420 samples from migratory birds and their surrounding environment were collected at three sites along the Qinghai Lake bird island. Carbapenem-non-susceptible isolates were identified by 16S rDNA sequencing and MALDI-TOF MS. Carbapenemase producers were determined by Carba NP testing. Antimicrobial susceptibility testing, transfer ability and PFGE were also performed, and 46 isolates from different pulsotypes were analysed by WGS.

Results

Three hundred and fifty isolates were carbapenemase producers based on Carba NP testing, while 233 Klebsiella spp. and 2 Escherichia coli isolates were NDM-5-carriers. PFGE was performed and showed that the isolates were grouped into five pulsotypes; among these, type A was predominant (86.7%, n = 202) and belonged to a novel Klebsiella lineage, ST1697. WGS analysis indicated that ST1697 strains may be a hybrid of the recombination of Klebsiella quasipneumoniae subsp. similipneumoniae and Klebsiella pneumoniae genomes.

Conclusions

This high frequency of carbapenemase producers in migratory birds is unexpected. These results provide new insight into the spread of antibiotic resistance, and highlight that continued vigilance for MDR carbapenemase-producing Enterobacteriaceae in migratory birds is urgently needed.

Issue Section: ORIGINAL RESEARCH

© The Author(s) 2019. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For permissions, please email: journals.permissions@oup.com.

This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model)

Keywords: Antibiotics; Drugs Resistance; Carbapenen; Wild Birds; Enterobacteriaceae; Klebsiella pneumoniae; China.

—–

#Serological Epidemiological #Investigation of Tibetan #Sheep (Ovis aries) #Plague in #Qinghai, #China (Vector Borne Zoo Dis., abstract)

[Source: Vector Borne and Zoonotic Diseases, full page: (LINK). Abstract, edited.]

Serological Epidemiological Investigation of Tibetan Sheep (Ovis aries) Plague in Qinghai, China

Ruixia Dai, Meiying Qi, Haoming Xiong, Xiaoyan Yang, Jian He, Zhikai Zhang, Hanqing Yang, Juan Jin, Xiang Li, Youquan Xin, Yonghai Yang, Cunxiang Li, Zhenjun Li, Jianguo Xu, Zuyun Wang, Wei Li, and Baiqing Wei

Published Online: 25 Sep 2018 / DOI: https://doi.org/10.1089/vbz.2017.2257

 

Abstract

The plague, which is caused by the Gram-negative coccobacillus bacterium Yersinia pestis, has been classified as a reemerging infectious disease by the World Health Organization. The Qinghai-Tibet Plateau natural plague focus is the largest plague focus in China, and Marmota himalayana is the primary host of the plague. Tibetan sheep (Ovis aries) were first identified as naturally infected hosts of Y. pestis based on etiological evidence in 1975, and activities such as slaughtering or skinning Tibetan sheep that have been infected by Y. pestis or died from Y. pestis infection had caused severe human plague in Qinghai. Tibetan sheep are important domestic livestock in the Qinghai-Tibet Plateau. Knowledge regarding the infection rate of Y. pestis in Tibetan sheep is important for understanding the range of infection and improving measures to control plague epidemics in this area. In this study, a serological survey involving 12,710 Tibetan sheep in all 44 counties in Qinghai Province was conducted. The total positive rate of indirect hemagglutination assay for Y. pestis in Tibetan sheep in Qinghai was 0.68% (86/12,710). Serological positivity to the Y. pestis F1 antibody was found in Tibetan sheep in all prefectures, except the Haidong and Haibei prefectures in Qinghai, with the seropositive rate in different counties ranging from 0.33% to 5.2% and the titers in the positive sera ranging from 1:20 to 1:5120. In addition, the seropositive rates in animal plague focus counties were higher than the rates in non-animal plague counties. Such results indicated a widespread infection of Tibetan sheep with Y. pestis in Qinghai, even though only sporadic epidemics of Tibetan sheep plague have been reported in Qinghai.

Keywords: Yersinia pestis; Plague; Sheeps; China; Tibet; Qinghai.

——

#Human #plague associated with Tibetan #sheep originates in #marmots (PLoS Negl Trop Dis., abstract)

[Source: PLoS Neglected Tropical Diseases, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Human plague associated with Tibetan sheep originates in marmots

Ruixia Dai , Baiqing Wei , Haoming Xiong, Xiaoyan Yang, Yao Peng, Jian He, Juan Jin, Yumeng Wang, Xi Zha, Zhikai Zhang, Ying Liang, Qingwen Zhang, Jianguo Xu, Zuyun Wang, Wei Li

Published: August 16, 2018 / DOI: https://doi.org/10.1371/journal.pntd.0006635

 

Abstract

The Qinghai-Tibet plateau is a natural plague focus and is the largest such focus in China. In this area, while Marmota himalayana is the primary host, a total of 18 human plague outbreaks associated with Tibetan sheep (78 cases with 47 deaths) have been reported on the Qinghai-Tibet plateau since 1956. All of the index infectious cases had an exposure history of slaughtering or skinning diseased or dead Tibetan sheep. In this study, we sequenced and compared 38 strains of Yersinia pestis isolated from different hosts, including humans, Tibetan sheep, and M. himalayana. Phylogenetic relationships were reconstructed based on genome-wide single-nucleotide polymorphisms identified from our isolates and reference strains. The phylogenetic relationships illustrated in our study, together with the finding that the Tibetan sheep plague clearly lagged behind the M. himalayana plague, and a previous study that identified the Tibetan sheep as a plague reservoir with high susceptibility and moderate sensitivity, indicated that the human plague was transmitted from Tibetan sheep, while the Tibetan sheep plague originated from marmots. Tibetan sheep may encounter this infection by contact with dead rodents or through being bitten by fleas originating from M. himalayanaduring local epizootics.

 

Author summary

Plague is mainly a disease of wild rodents, and their parasitic fleas are considered the transmitting vectors. However, human plague originating from Ovis aries (Tibetan sheep) is found in the Qinghai-Tibet plateau in China, where Marmota. himalayana is the primary plague host. Tibetan sheep-related human plague infection is always associated with slaughtering or skinning diseased or dead Tibetan sheep. The plague in Tibetan sheep clearly lags that in M. himalayana. In this study, we performed a genome-wide single nucleotide polymorphism analysis of Tibetan sheep-related plague events, including pathogens isolated from humans, Tibetan sheep, and marmots. Through genomic analysis, together with the epidemiological connections, we confirmed that human plague came from Tibetan sheep, and the Tibetan sheep plague originated from marmots. Tibetan sheep account for about 1/3 of the total number of sheep in China. Tibetan sheep and goats are important domestic livestock on the Qinghai-Tibet plateau. Therefore, the hazards of Tibetan sheep plague should not be underestimated.

___

Citation: Dai R, Wei B, Xiong H, Yang X, Peng Y, He J, et al. (2018) Human plague associated with Tibetan sheep originates in marmots. PLoS Negl Trop Dis 12(8): e0006635. https://doi.org/10.1371/journal.pntd.0006635

Editor: Didier Raoult, Faculté de Médecine,Aix-Marseille Université, FRANCE

Received: April 21, 2018; Accepted: June 25, 2018; Published: August 16, 2018

Copyright: © 2018 Dai et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: This work was supported by grants from the National Natural Science Foundation of China (81260438 and 81290340), a Provincial Applied Basic Research Project of Qinghai (2016-ZJ-789), and a National Priority Development Project on Key Science Instruments (2012YQ09019706). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Yersinia Pestis; Plague; Human; Sheep; Wildlife; China; Tibet.

——

#Genetic diversity and spatial-temporal #distribution of #Yersinia pestis in #Qinghai Plateau, #China (PLoS Negl Trop Dis., abstract)

[Source: PLoS Neglected Tropical Diseases, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Genetic diversity and spatial-temporal distribution of Yersinia pestis in Qinghai Plateau, China

Xiaoqing Xu , Yujun Cui , Youquan Xin, Xiaoyan Yang, Qingwen Zhang, Yong Jin, Haihong Zhao, Jian He, Xing Jin, Cunxiang Li, Juan Jin, Xiang Li, Haisheng Wu, Zhizhen Qi

Published: June 25, 2018 / DOI: https://doi.org/10.1371/journal.pntd.0006579 / This is an uncorrected proof.

 

Abstract

Background

Plague, caused by the bacterium Yersinia pestis, is a highly infectious, zoonotic disease. Hundreds of human plague cases are reported across the world annually. Qinghai Plateau is one of the most severely affected plague regions in China, with more than 240 fatal cases of Y. pestis in the last 60 years. Conventional epidemiologic analysis has effectively guided the prevention and control of local plague transmission; however, molecular genetic analysis is more effective for investigating population diversity and transmission. In this report, we employed different genetic markers to analyze the population structure of Y. pestis in Qinghai Plateau.

Methodology/Principal finding

We employed a two-step hierarchical strategy to analyze the phylogeny of 102 Qinghai Plateau isolates of Y. pestis, collected between 1954 and 2011. First, we defined the genealogy of Y. pestis by constructed minimum spanning tree based on 25 key SNPs. Seven groups were identifi7ed, with group 1.IN2 being identified as the dominant population. Second, two methods, MLVA and CRISPR, were applied to examine the phylogenetic detail of group 1.IN2, which was further divided into three subgroups. Subgroups of 1.IN2 revealed a clear geographic cluster, possibly associated with interaction between bacteriophage and Y. pestis. More recently, Y. pestis populations appear to have shifted from the east toward the center and west of Qinghai Plateau. This shift could be related to destruction of the local niche of the original plague focus through human activities. Additionally, we found that the abundance and relative proportion of 1.IN2 subgroups varied by decade and might be responsible for the fluctuations of plague epidemics in Qinghai Plateau.

Conclusion/Significance

Molecular genotyping methods provided us with detailed information on population diversity and the spatial-temporal distribution of dominant populations of Y. pestis, which will facilitate future surveillance, prevention, and control of plague in Qinghai Plateau.

 

Author summary

Plague is a highly infectious disease caused by the Yersinia pestis bacterium. Since the first strain of Y. pestis was isolated in Qinghai in 1954, confirmed plague cases have occurred nearly every year, and more than 240 people have died from plague over the past 60 years. In this study, we analyzed 102 Y. pestis strains collected from Qinghai Plateau between 1954 and 2011. We determined their genetic diversity and inferred their spatial-temporal distribution, based on genetic markers including SNPs, VNTRs and CRISPRs. Our results indicate that 1.IN2 is the dominant group of Y. pestis in Qinghai Plateau, and its three subpopulations revealed clear geographic clustering that might be driven by interaction with bacteriophages. We observed that the Y. pestis population has moved from the east of Qinghai Plateau to central and western regions over the past 60 years. We also found that the abundance and relative proportion of 1.IN2 subgroups varied over time, leading to fluctuations in plague epidemics. These results extend our knowledge of the genetic diversity of Y. pestis, and its population dynamics in natural plague foci over a number of years. With ongoing risk of outbreaks, we recommend enhanced surveillance in this region.

___

Citation: Xu X, Cui Y, Xin Y, Yang X, Zhang Q, Jin Y, et al. (2018) Genetic diversity and spatial-temporal distribution of Yersinia pestis in Qinghai Plateau, China. PLoS Negl Trop Dis 12(6): e0006579. https://doi.org/10.1371/journal.pntd.0006579

Editor: Stephen W. Attwood, Sichuan University, CHINA

Received: November 13, 2017; Accepted: June 4, 2018; Published: June 25, 2018

Copyright: © 2018 Xu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: This work was supported by Natural Science Foundation of Qinghai Province, China (2013-Z-906) and National Natural Science Foundation of China (31470138). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Keywords: Plague; Yersinia Pestis; China; Qinghai.

——