Circulation, #Evolution and #Transmission of Highly Pathogenic #Avian #Influenza A (#H5N8) virus, 2016-2018 (J Infect., abstract)

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

J Infect. 2019 Jul 12. pii: S0163-4453(19)30214-2. doi: 10.1016/j.jinf.2019.07.005. [Epub ahead of print]

Circulation, Evolution and Transmission of Highly Pathogenic Avian Influenza A (H5N8) virus, 2016-2018.

Chen J1, Liang B2, Hu J3, Liu H3, Sun J4, Li M5, Chen Q6, He Y4, Liu D7.

Author information: 1 CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; Center for Influenza Research and Early warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China. Electronic address: chenjj@wh.iov.cn. 2 CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy Sciences, Beijing, 101409, China. 3 CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. 4 Qinghai Lake National Nature Reserve, Xining, 810099, China. 5 CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China. 6 CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; Center for Influenza Research and Early warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China. 7 CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; Center for Influenza Research and Early warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, China; University of Chinese Academy Sciences, Beijing, 101409, China. Electronic address: liud@wh.iov.cn.

 

Abstract

OBJECTIVES:

A second wave of highly pathogenic avian influenza A virus (HPAIV) H5N8 clade 2.3.4.4 has spread globally, causing outbreaks among wild birds and domestic poultry since autumn 2016. The circulation and evolutionary dynamics of the virus remain largely unknown.

METHODS:

We performed surveillance for H5N8 in Qinghai Lake in China since the emergence of the virus (from 2016 to 2018). By analyzing recovered viruses in Qinghai Lake and all related viruses worldwide (449 strains), we identified the genotypes, estimated their genesis and reassortment, and evaluated their global distribution and transmission.

RESULTS:

Through surveillance of wild migratory birds around Qinghai Lake between 2016 and 2018, we revealed that the H5N8 was introduced into Qinghai Lake bird populations (QH-H5N8), with distinct gene constellations in 2016 and 2017. A global analysis of QH-H5N8-related viruses showed that avian influenza viruses with low pathogenicity in wild birds contributed to the high diversity of genotypes; the major reassortment events possibly occurred during the 2016 breeding season and the following winters.

CONCLUSIONS:

Continued circulation of QH-H5N8-related viruses among wild birds has resulted in the global distribution of high genotypic diversity. Thus, these viruses pose an ongoing threat to wild and domestic bird populations and warrant continuous surveillance.

Copyright © 2019. Published by Elsevier Ltd.

KEYWORDS: Circulation; Evolution; H5N8 avian influenza; Migratory birds; Transmission

PMID: 31306679 DOI: 10.1016/j.jinf.2019.07.005

Keywords: Avian Influenza; H5N8; Poultry; Wild Birds.

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#Plasmid-Mediated #mcr-1 #Colistin #Resistance in #Escherichia coli from a Black Kite in #Russia (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Plasmid-Mediated mcr-1 Colistin Resistance in Escherichia coli from a Black Kite in Russia

Hassan Tarabai, Adam Valcek, Ivana Jamborova, Sergey V. Vazhov, Igor V. Karyakin, Rainer Raab, Ivan Literak, Monika Dolejska

DOI: 10.1128/AAC.01266-19

 

ABSTRACT

The gene mcr-1 conferring resistance to last-line antibiotic colistin has been reported globally. Here we describe the first detection of plasmid-mediated colistin resistance in Russian wildlife, an isolate of Escherichia coli sequence type 2280 from a black kite (Milvus migrans), scavenging raptor. Whole genome sequencing and plasmid transferability experiments revealed that mcr-1.1 was located on a conjugative IncI2 plasmid pDR164 (59891 bp). Migratory Black Kites may contribute to the global spread of mobile colistin resistance.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; Colistin; MCR1; E. Coli; Wild Birds; Russia.

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#Resistance to critically important #antimicrobials in #Australian silver #gulls (Chroicocephalus novaehollandiae) and evidence of #anthropogenic origins (J Antimicrob Chemother., abstract)

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

Resistance to critically important antimicrobials in Australian silver gulls (Chroicocephalus novaehollandiae) and evidence of anthropogenic origins

Shewli Mukerji, Marc Stegger, Alec Vincent Truswell, Tanya Laird, David Jordan, Rebecca Jane Abraham, Ali Harb, Mary Barton, Mark O’Dea, Sam Abraham

Journal of Antimicrobial Chemotherapy, dkz242, https://doi.org/10.1093/jac/dkz242

Published: 09 July 2019

 

Abstract

Objectives

Antimicrobial resistance (AMR) to critically important antimicrobials (CIAs) amongst Gram-negative bacteria can feasibly be transferred amongst wildlife, humans and domestic animals. This study investigated the ecology, epidemiology and origins of CIA-resistant Escherichia coli carried by Australian silver gulls (Chroicocephalus novaehollandiae), a gregarious avian wildlife species that is a common inhabitant of coastal areas with high levels of human contact.

Methods

Sampling locations were widely dispersed around the perimeter of the Australian continent, with sites separated by up to 3500 km. WGS was used to study the diversity and molecular characteristics of resistant isolates to ascertain their epidemiological origin.

Results

Investigation of 562 faecal samples revealed widespread occurrence of extended-spectrum cephalosporin-resistant (21.7%) and fluoroquinolone-resistant (23.8%) E. coli. Genome sequencing revealed that CIA-resistant E. coliisolates (n = 284) from gulls predominantly belonged to human-associated extra-intestinal pathogenic E. coli (ExPEC) clones, including ST131 (17%), ST10 (8%), ST1193 (6%), ST69 (5%) and ST38 (4%). Genomic analysis revealed that gulls carry pandemic ExPEC-ST131 clades (O25:H4 H30-R and H30-Rx) and globally emerging fluoroquinolone-resistant ST1193 identified among humans worldwide. Comparative analysis revealed that ST131 and ST1193 isolates from gulls overlapped extensively with human clinical isolates from Australia and overseas. The present study also detected single isolates of carbapenem-resistant E. coli (ST410-blaOXA-48) and colistin-resistant E. coli (ST345-mcr-1).

Conclusions

The carriage of diverse CIA-resistant E. coli clones that strongly resemble pathogenic clones from humans suggests that gulls can act as ecological sponges indiscriminately accumulating and disseminating CIA-resistant bacteria over vast distances.

Topic: colistin – epidemiology – animals, domestic – australia – aves – clone cells – disease transmission – drug resistance, microbial – ecology – feces – fluoroquinolones – genome – gram-negative bacteria – intestines – prescriptions, drug – surgical sponges – bacteria – silver – antimicrobials – escherichia coli – pandemics – genome sequencing – carbapenem resistance – extraintestinal pathogenic escherichia coli – whole genome sequencing

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; Carbapenem; Colistin; Fluoroquinolones; MCR1; E.Coli; Wild Birds; Australia.

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#Prevalence of #avian #influenza viruses and their associated #antibodies in #wildbirds in #China: A systematic review and meta-analysis (Microb Pathog., abstract)

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

Microb Pathog. 2019 Jun 26:103613. doi: 10.1016/j.micpath.2019.103613. [Epub ahead of print]

Prevalence of avian influenza viruses and their associated antibodies in wild birds in China: A systematic review and meta-analysis.

Chen X1, Li C2, Sun HT3, Ma J2, Qi Y4, Qin SY5.

Author information: 1 College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, PR China; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China. 2 College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China. 3 General Monitoring Station for Wildlife-borne Infectious Diseases, State Forestry and Grassland Administration, Liaoning, Shenyang, 110034, PR China. 4 College of Animal Science, Anhui Science and Technology University, Fengyang, 233100, PR China; College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, PR China. Electronic address: qypandcxl@163.com. 5 General Monitoring Station for Wildlife-borne Infectious Diseases, State Forestry and Grassland Administration, Liaoning, Shenyang, 110034, PR China. Electronic address: qinsiyuan0303@126.com.

 

Abstract

Avian influenza viruses (AIVs) in wild birds pose a pandemic threat to humans and to the poultry industry. To assess AIV and AIV antibody prevalence in wild birds in China, a systematic review and meta-analysis were conducted. We searched PubMed, Google Scholar, Cochrane Library, Clinical Trial, VIP, CNKI, and WANFANG for published papers related to the prevalence of AIVs and their associated antibodies in wild birds in China from Mar. 10, 2005 to Sept. 20, 2018. Repeat studies, reviews, and other host studies were excluded, as well as those with inconsistent data, incomplete information, or only prevalence data or data from outside of mainland China. In total, data from 28 publications were compiled and analyzed. Based on out meta-analysis, the pooled prevalence of AIVs in wild birds in China was found to be 2.5% (571/23,024), and the pooled prevalence of AIV antibodies was 26.5% (1,210/4,566). The pooled prevalence of AIVs was significantly higher in wild birds from Central China (5.5%, 271/4, 955) compared to all other regions and the pooled prevalence of AIV antibodies was significantly in wild birds from South China (56.8%, 92/162) in comparison to all other regions. The prevalence of both AIVs and AIV antibodies in Anseriformes were higher compared to non-Anseriformes. In addition, the largest number of studies found in this review were on the HA subtypes of AIVs (H5, H7, and H9) and their associated antibodies. In summary, our findings suggest that the prevalence of AIVs and their antibodies in wild birds vary among regions and species of wild bird. Thus, further monitoring of the prevalence of AIVs and their antibodies in wild birds in China is necessary and should be used for guiding powerful and effective regulatory measures that will prevent the spread of AIVs across species.

Copyright © 2019. Published by Elsevier Ltd.

KEYWORDS: AIV; AIV antibody; Epidemiology; Pandemic; Transspecies; Wild birds

PMID: 31254602 DOI: 10.1016/j.micpath.2019.103613

Keywords: Avian Influenza; Seroprevalence; Wild Birds; China.

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Clade 2.3.4.4 #H5 North #American Highly Pathogenic #Avian #Influenza Viruses Infect, but Do Not Cause #Clinical Signs in, American Black #Ducks (Anas rubripes) (Avian Dis., abstract)

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

Avian Dis. 2019 Jan 18;63(2):366-370. doi: 10.1637/11950-081418-ResNote.1.

Clade 2.3.4.4 H5 North American Highly Pathogenic Avian Influenza Viruses Infect, but Do Not Cause Clinical Signs in, American Black Ducks (Anas rubripes).

Spackman E1, Prosser DJ2, Pantin-Jackwood M3, Stephens CB3, Berlin AM2.

Author information: 1 Southeast Poultry Research Laboratory, United States National Poultry Research Center, United States Department of Agriculture, Agricultural Research Service, Athens, GA 30605, erica.spackman@ars.usda.gov. 2 Patuxent Wildlife Research Center, United States Geological Survey, Laurel, MD 20708. 3 Southeast Poultry Research Laboratory, United States National Poultry Research Center, United States Department of Agriculture, Agricultural Research Service, Athens, GA 30605.

 

Abstract in English, Spanish

Highly pathogenic avian influenza virus (HPAIV) from the goose/Guangdong/1996 clade 2.3.4.4 H5 lineage spread from Asia into North America in 2014, most likely by wild bird migrations. Although several variants of the virus were detected, H5N8 and H5N2 were the most widespread in North American wild birds and domestic poultry. In early 2015, the H5N2 virus spread through commercial poultry in the Midwest, and >50 million chickens and turkeys died or had to be culled. Related H5 HPAIVs are still endemic in much of the Eastern Hemisphere. The wild bird species that were involved with dissemination of the virus in North America are not known. Dabbling ducks, especially mallards (Anas platyrhynchos), typically have the highest detection rates for avian influenza viruses. To better characterize the wild avian species that could spread the virus, American black ducks (Anas rubripes), which are closely related to mallards, were challenged with the North American H5N2 and H5N8 index HPAIV isolates: A/Northern Pintail/WA/40964/2014 H5N2 and A/Gyrfalcon/WA/41088/2014 H5N8. Although the American black ducks could be infected with low doses of both isolates (≤102 50% egg infective doses), ducks shed the H5N2 longer than the H5N8 (10 vs. 7 days) and the titers of virus shed were higher. Although there were too few ducks available on which to draw definitive conclusions, this suggests that American black ducks could serve as a more efficient reservoir for the H5N2 virus than the H5N8 virus.

KEYWORDS: H5 influenza; avian virus; duck virus; highly pathogenic avian influenza virus

PMID: 31251539 DOI: 10.1637/11950-081418-ResNote.1

Keywords: Avian Influenza; H5N2; H5N8; Reassortant strain; Wild Birds; USA.

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#Phylogeographic #evidence for the inter- and intra- #continental #dissemination of #avian #influenza viruses via #migration #flyways (PLoS One, abstract)

[Source: PLoS One, full page: (LINK). Abstract, edited.]

OPEN ACCESS /  PEER-REVIEWED / RESEARCH ARTICLE

Phylogeographic evidence for the inter- and intracontinental dissemination of avian influenza viruses via migration flyways

Junki Mine, Yuko Uchida, Kirill Sharshov, Ivan Sobolev, Alexander Shestopalov, Takehiko Saito

Published: June 26, 2019 / DOI: https://doi.org/10.1371/journal.pone.0218506

 

Abstract

Genetically related highly pathogenic avian influenza viruses (HPAIVs) of H5N6 subtype caused outbreaks simultaneously in East Asia and Europe—geographically distinct regions—during winter 2017–2018. This situation prompted us to consider whether the application of phylogeographic analysis to a particular gene segment of AIVs could provide clues for understanding how AIV had been disseminated across the continent. Here, the N6 NA genes of influenza viruses isolated across the world were subjected to phylogeographic analysis to illustrate the inter- and intracontinental dissemination of AIVs. Those isolated in East Asia during winter and in Mongolia/Siberia during summer were comingled within particular clades of the phylogeographic tree. For AIVs in one clade, their dissemination in eastern Eurasia extended from Yakutia, Russia, in the north to East Asia in the south. AIVs in western Asia, Europe, and Mongolia were also comingled within other clades, indicating that Mongolia/Siberia plays an important role in the dissemination of AIVs across the Eurasian continent. Mongolia/Siberia may therefore have played a role in the simultaneous outbreaks of H5N6 HPAIVs in Europe and East Asia during the winter of 2017–2018. In addition to the long-distance intracontinental disseminations described above, intercontinental disseminations of AIVs between Eurasia and Africa and between Eurasia and North America were also observed. Integrating these results and known migration flyways suggested that the migration of wild birds and the overlap of flyways, such as that observed in Mongolia/Siberia and along the Alaskan Peninsula, contributed to the long-distance intra- and intercontinental dissemination of AIVs. These findings highlight the importance of understanding the movement of migratory birds and the dynamics of AIVs in breeding areas—especially where several migration flyways overlap—in forecasting outbreaks caused by HPAIVs.

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Citation: Mine J, Uchida Y, Sharshov K, Sobolev I, Shestopalov A, Saito T (2019) Phylogeographic evidence for the inter- and intracontinental dissemination of avian influenza viruses via migration flyways. PLoS ONE 14(6): e0218506. https://doi.org/10.1371/journal.pone.0218506

Editor: Charles J. Russell, St. Jude Children’s Research Hospital, UNITED STATES

Received: April 12, 2019; Accepted: June 4, 2019; Published: June 26, 2019

Copyright: © 2019 Mine 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 sequence data are available from the GISAID database (accession numbers are listed in S1 Table).

Funding: This study was supported in part by a research project grant from the “Pilot program of international collaborative research (Collaborative research based on a joint call with Russia)” under “Commissioned projects for promotion of strategic international collaborative research,” a grant from the Agriculture, Forestry and Fisheries Research Council (JP) and a grant from the Russian Scientific Foundation (project # 17-44-07001). 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: Avian Influenza; H5N6; Wild Birds.

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Repeated detection of #carbapenemase-producing #Escherichia coli in #gulls inhabiting #Alaska, #USA (Antimicrob Agents Chemother., abstract)

[Source: Antimicrobial Agents and Chemotherapy, full page: (LINK). Abstract, edited.]

Repeated detection of carbapenemase-producing Escherichia coli in gulls inhabiting Alaska, USA

Christina A. Ahlstrom, Andrew M. Ramey, Hanna Woksepp, Jonas Bonnedahl

DOI: 10.1128/AAC.00758-19

 

ABSTRACT

We report the first detection of carbapenemase-producing Escherichia coli in Alaska and in wildlife in the United States. Wild bird (gull) feces sampled at three locations in Southcentral Alaska yielded isolates that harbored plasmid-encoded blaKPC-2 or chromosomally-encoded blaOXA-48, and genes associated with antimicrobial resistance to up to eight antibiotic classes.

Copyright © 2019 American Society for Microbiology. All Rights Reserved.

Keywords: Antibiotics; Drugs Resistance; Carbapenem; E. Coli; Wild birds; Alaska; USA.

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