The role of wildlife (wild birds)in the global transmission of antimicrobial resistance genes

Antimicrobial resistance is an urgent global health challenge in human and veterinary medicine. Wild animals are not directly exposed to clinically relevant antibiotics; however, antibacterial resistance in wild animals has been increasingly reported worldwide in parallel to the situation in human and veterinary medicine. This underlies the complexity of bacterial resistance in wild animals and the possible interspecies transmission between humans, domestic animals, the environment, and wildlife. This review summarizes the current data on expanded- spectrum 13-1actamase （ESBL）, AmpC IB-lactamase, carbapenemase, and colistin resistance genes in Enterobacteriaceae isolates of wildlife origin. The aim of this review is to better understand the important role of wild animals as reservoirs and vectors in the global dissemination of crucial clinical antibacterial resistance. In this regard, continued surveillance is urgently needed worldwide.

Response to Comment on "The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes"

DEAR EDITOR,Since our first identification of plasmid-mediated colistin resistance gene mcr-1 in 2015 （Liu et al., 2016）, it has been described in human clinics, domestic animals, foods, and the environment worldwide （Schwarz ＆ Johnson, 2016）. Although it is still rare, the emergence of mcr-I in wild animals is of great concern. We summarized two previous reports on mcr-1 in wild birds from Lithuania and Argentina to describe its emergence and characteristics in wildlife and highlight the potentially important role of wild animals, particularly birds, in its global transmission （Wang et al., 2017）. The first detection of mcr-1 in wildlife in Asia was identified in an extended-spectrum β- lactamase-producing Escherichia coil strain isolated from Eurasian coot （Fulica atra）,

Risk Analysis of Wild Birds in Spread of Highly Pathogenic Avian Influenza

Outbreaks of highly pathogenic avian influenza （HPAI） H5N 1 have taken place in 15 countries in Asia, Europe and Africa since 2003, and have caused great economic losses. Much likelihood has been considered as risk factors, of which wild birds are attributed as one of the main factors. This is related to the environmental deterioration in the wetland and expanse of human＇s activities in production. The risk analysis in this paper only focused on the effect of wild birds to HPAI, and confirmed the high risk of wild birds in the spread of AIVs.

Avian influenza virus ecology in wild birds of Western Siberia

Background:The aim of the study was to explore the ecological diversity of wild birds in Siberia, which are the natural reservoir of avian influenza virus(AIV).Methods:Cloacal swabs and intestinal fragments were collected from wild migratory birds from 2007-2014. Isolated viruses were grown in the allantoic cavity of embryonated chicken eggs. The presence of virus was determined using hemagglutination assays. Primary identification and subtyping of influenza viruses was confirmed by RT-PCR.Results:A total of 2300 samples obtained from wild migratory birds of 8 orders were collected and tested. Influenza was detected in 185 birds of 3 orders. Species of family Anatidae(order Anseriformes) such as European Teal(Anas crecca), Garganey Teal(A. querquedula), and Shoveler(A. clypeata) play the main role in AIV circulation in the south of Western Siberia. The proportion of viral carriers among waterfowl ranged from 5.6 to 20% in 2007-2014. The order Charadriiformes had lower virus isolation rates of not more than 1.4%.Conclusions:Wild migratory waterfowl of orders Anseriformes and Charadriiformes are the main reservoir of AIV in the south of Western Siberia. This area plays a key role in persistence, evolution, and geographical distribution of avian influenza.

Comment on ＂The role of wildlife (wild birds)in the global transmission of antimicrobial resistance genes＂

DEAR EDITOR, We read with interest the article by Wang and colleagues regarding the role of wildlife in the transmission of antimicrobial resistance （AMR） （Wang et al., 2017）. Although we appreciate the efforts in reviewing this important topic, we would like to comment on some statements that we believe are not up-to- date or properly cited.

Results of the influenza virus surveillance in wild birds in Western part of Mongolia

Objective:To present results of virological study of wild birds inhabiting Western Mongolia. Methods:Over a period of 2003-2008,we isolated 13 influenza A viruses:H1N1,H3N6, H13N8 and H4N6 subtypes.We did not isolate any H5N1 subtype,that still cause epizooty in wild birds and poultry.Results:We revealed taxonomic and ecological heterogeneity of the birds involved in maintenance of circulation of influenza viruses in the given territory.Influenza viruses were isolated from birds of 6 orders;among them there are species preferring water and semi-aquatic biotopes,one species preferring dry plain region,and also one species which can inhabit both dry and water biotopes.Conclusions:Representatives of all main orders of Western Mongolia avifauna are involved in support of influenza A virus circulation,highly pathogenic H5N1 influenza viruses were registered in Mongolia thus it’s necessary to continue permanent influenza virus surveillance in wild birds’ populations.

Occurrence of Chlamydia spp.in wild birds in Thailand

Objective: To determine the occurrence of Chlamydia spp.in wild birds in Thailand.Methods: Cloacal and tracheal swabs of 313 wild birds from 11 orders, 27 families, and 51 species were tested to determine the occurrence of Chlamydia infection.The outer membrane protein A(ompA) gene was amplified from positive samples to construct a phylogenetic tree.Results: At the time of sample collection, none of the birds showed clinical signs of any disease.Of 313 wild birds, two Asian openbill stork(Anastomus oscitans) were positive for Chlamydia spp., representing 0.64%(2/313) and 4.9%(2/41) occurrence for birds overall and for the Asian openbill stork, respectively.Phylogram analysis based on deduced amino acid of the ompA gene showed that Chlamydia spp.in Asian openbill storks was closely related to that in wildfowl(Pica pica and Cygnus olor) from Poland in a different branch with a 95% bootstrap value and had a shorter evolutionary distance to Chlamydia abortus.Conclusions: Asymptomatic Asian openbill storks could be a potential source of Chlamydia infection in domestic animals, poultry, and humans who share their habitat.

Occurrence of Escherichia coli virulence genes in feces of wild birds from Central Italy

Objective: To investigate the potential role of wild birds as fecal spreaders of enteropathogenic,enterohemorrhagic and Shiga-toxins producing Escherichia coli(E. coli),enteropathogenic E. coli,enterohemorrhagic E. coli and Shiga toxin-producing E. coli strains. Methods: Fecal samples collected from 121 wild birds of different orders and species were submitted to molecular analyses. In particular,eaeA encoding intimin,hlyA encoding for hemolysin,stx1 and stx2 genes encoding Shiga-toxins 1 and 2,respectively,were investigated. Results: Overall,21(17.35%) fecal samples resulted positive for at least one of the investigated genes. In detail,12(9.91%) samples were positive for eaeA,10(8.26%) for stx1,4(3.31%) for hylA and 1(0.83%) for stx2. An owl(Athene noctua) positive for the four investigated genes suggesting that it harbored a STEC strain. However,virulence genes characterizing EPEC,and EHEC strains were mainly found among seagulls,waterfowl and feral pigeons. Conclusions: Seagulls,waterfowl and feral pigeons,which frequently reach and contaminate rural,urban and peri-urban areas with their droppings,may be important sources of E. coli infection for other animals and humans.

Diversity of coronaviruses in wild and domestic birds in Vietnam

Objective:To investigate the genetic diversity of coronaviruses in wild and domestic birds in the bird park and live poultry markets of Ca Mau province in Vietnam in 2020.Methods:A total of 228 samples(121 from wild birds and 107 from poultry)were collected in the territory of Ca Mau province of Vietnam in 2020.The avian samples were tested for the presence of the four genera of coronaviruses using reverse transcription and nested PCR.Molecular genetic analysis using targeted NGS sequencing of RdRp gene was performed for 29 representative samples(12 samples from wild birds and 17 from poultry).Phylogenetic analysis was performed using the neighbour joininig method with 1000 bootstrap replications using MEGA X software.Results:Among wild birds,21.5%samples were positive for the genetic material of coronaviruses and 38.3%samples were positive for coronaviruses among poultry.Genetic analysis of the partial sequence of RdRp gene from representative samples revealed that wild birds were carriers of gammacoronaviruses and deltacoronaviruses.Among poultry,three genotypes of infectious bronchitis virus(QX,Mass and Q1)were detected in chickens,with QX genotypes being predominant,and viruses of DCoV group were detected in domestic ducks.There was no detection of alphacoronaviruses or betacoronaviruses in the studied birds.Conclusions:Coronaviruses of genera Gammacoronavirus and Deltacoronavirus were detected in wild birds.A high percentage of infectious bronchitis virus was detected in poultry.Thus,there is a need for broader surveillance of coronaviruses in birds,which can be used for evaluation of diversity,evolution and distribution of coronaviruses in Vietnam.Continuous surveillance of coronaviruses circulation in wild and domestic animals is necessary for implementing strategic measures for poultry and domestic animal protection and for evaluation of possible risk of circulating coronaviruses to human health.

Canada’s inter-agency wild bird influenza survey

Canada’s Inter-agency Wild Bird Influenza Survey,which started in 2005,and is a collaborative effort among federal,provincial and territorial government agencies as well as non-governmental organizations and academic institutions,has two components:(i)a seasonal survey of live wild waterfowl species from selected geographic regions across Canada(to expand our understanding of the avian influenza viruses circulating in wild bird populations);and(ii)an ongoing survey of birds found dead that are submitted to a regional diagnostic laboratory(to enhance detection of highly pathogenic avian influenza strains).Combined swabs from the cloaca and oro-pharynx collected from each bird are screened using a real-time reverse transcriptase-polymerase chain reaction(RRT-PCR)that targets a unique segment of the influenza A M1 gene.If the M1 result is positive or inconclusive,RRT-PCR for gene segments of the H5 and H7 hemagglutinin subtypes are performed.All samples that are RRT-PCR positive for H5 or H7 are sent immediately for test confirmation and further characterization.All field and laboratory data are entered into a database developed and maintained by the Canadian Cooperative Wildlife Health Centre.Since the survey commenced in 2005,on average,30%of all live ducks sampled,5%of other species of live birds and 3%of birds found dead have tested positive for avian influenza,all of North American lineage and of low pathogenicity.

Surveillance for highly pathogenic avian influenza in wild birds in the USA

As part of the USA’s National Strategy for Pandemic Influenza,an Interagency Strategic Plan for the Early Detection of Highly Pathogenic H5N1 Avian Influenza in Wild Migratory Birds was developed and implemented.From1April2006 through 31 March 2009,261946 samples fromwild birds and 101457 wild bird fecalsamples were collected in the USA;no highly pathogenic avian influenza was detected.The United States Department of Agriculture,and state and tribal cooperators accounted for 213115(81%)of the wild bird samples collected;31,27,21 and 21%of the samples were collected from theAtlantic,Pacific,Central and Mississippi flyways,respectively.More than 250 species of wild birds in all 50 states were sampled.The majority of wild birds(86%)were dabbling ducks,geese,swans and shorebirds.The apparent prevalence of low pathogenic avian influenza viruses during biological years 2007 and 2008 was 9.7 and 11.0%,respectively.The apparent prevalence of H5 and H7 subtypes across all species sampled were 0.5 and 0.06%,respectively.The pooled fecal samples(n=101539)positive for low pathogenic avian influenza were 4.0,6.7 and 4.7%for biological years 2006,2007 and 2008,respectively.The highly pathogenic early detection system for wild birds developed and implemented in the USA represents the largest coordinated wildlife disease surveillance system ever conducted.This effort provided evidence that wild birds in the USA were free of highly pathogenic avian influenza virus(given the expected minimum prevalence of 0.001%)at the 99.9%confidence level during the surveillance period.

Metagenomic Analysis of Environmental Samples from Wildlife Rescue Station at Poyang Lake, China

Objective To improve the understanding of the virome and bacterial microbiome in the wildlife rescue station of Poyang Lake,China.Methods Ten smear samples were collected in March 2019.Metagenomic sequencing was performed to delineate bacterial and viral diversity.Taxonomic analysis was performed using the Kraken2 and Bracken methods.A maximum-likelihood tree was constructed based on the RNA-dependent RNA polymerase(RdRp)region of picornavirus.Results We identified 363 bacterial and 6 viral families.A significant difference in microbial and viral abundance was found between samples S01–S09 and S10.In S01–S09,members of Flavobacteriia and Gammaproteobacteria were the most prevalent,while in S10,the most prevalent bacteria class was Actinomycetia.Among S01–S09,members of Myoviridae and Herelleviridae were the most prevalent,while the dominant virus family of S10 was Picornaviridae.The full genome of the pigeon mesivirus-like virus(NC-BM-233)was recovered from S10 and contained an open reading frame of 8,124 nt.It showed the best hit to the pigeon mesivirus 2 polyprotein,with 84.10%amino acid identity.Phylogenetic analysis showed that RdRp clustered into Megrivirus B.Conclusion This study provides an initial assessment of the bacteria and viruses in the cage-smeared samples,broadens our knowledge of viral and bacterial diversity,and is a way to discover potential pathogens in wild birds .

野生鸟类经济价值评估——以海南新盈红树林国家湿地公园鸟类为例

开展生物多样性尤其是野生鸟类经济价值评估是一项非常有意义而又难度较高的工作。本研究基于2017年颁布的《野生动物及其制品价值评估方法》中提供的相关鸟类基准价及其整体价值估算方法,利用文献提供的鸟类现场调查数据,并根据其最新的保护级别和濒危等级,对其基准价进行调整优化,量化了海南新盈红树林国家湿地公园2016年春、夏、秋、冬四季调查所发现鸟类的经济价值,结果发现:2016年春、夏、秋、冬4个季节调查发现的鸟类估值分别为144.28万元、13.00万元、1 043.82万元和1 044.99万元(2017年价),各季节间表现出较大差异。新盈红树林国家湿地公园对鸟类的承载作用冬季最大,秋季次之,夏季最小。从不同鸟类价值贡献看,重点应关注的鸟类为勺嘴鹬和黑脸琵鹭2种国家一级保护动物,其次是白鹭、大白鹭、中杓鹬和蒙古沙鸻等数量较多的鸟类。本研究提出的估值方法和传统生物多样性评估联合使用可更好了解调查区鸟类保护价值及其变化。

黄河三角洲湿地野生鸟类多样性分析及协同治理策略研究

黄河三角洲湿地是中国保护最完善的湿地生态系统之一,对其野生鸟类多样性分析及实行协同治理具有重要意义,因此,提出黄河三角洲湿地野生鸟类多样性分析及协同治理策略研究。介绍黄河三角洲湿地区域,以香农一韦弗多样性指数、属-科综合多样性指数等指数为评估指标,分析黄河三角洲湿地野生鸟类多样性。对黄河三角洲湿地的野生鸟类展开调研和多样性分析,得出该湿地对鸟类繁殖及迁移起到重要作用,并且荒滩草地鸟类的非单种科较多,村庄农田和荒滩草地的鸟类相似性最高。根据分析结果,提出黄河三角洲湿地的协同治理策略。

野生鸟类介导抗生素抗性基因传播的研究进展

细菌的抗生素耐药是重大的公共卫生问题,抗生素抗性基因(antibiotic resistance genes, ARGs)可能会在人类、动物和环境微生物组之间水平转移,使其相互依存的生态系统与公共卫生之间存在潜在关联性。鸟类是地球上种类繁多的物种之一,它们的跨距离传播可能会加速耐药基因在全球范围内的扩展,带来一定的健康风险。本文综述了野生鸟类介导抗生素抗性基因在生态环境中的主动传播,提出其作为传播媒介的重要性,并分别阐述了城市留鸟和候鸟对抗生素抗性基因的传播作用,着重突出了候鸟跨地区传播的作用,总结出野生鸟类介导抗生素抗性基因的传播是尤为重要的研究方向。

云南野鸟源H9N2亚型AIV的遗传进化分析

【目的】分析云南纳帕海国际重要湿地H9N2亚型禽流感病毒(Avian influenza virus,AIV)的遗传进化和分子特征,掌握H9N2亚型AIV在野禽中的流行特点,为禽流感疫情防控提供数据支持。【方法】采集2022―2023年云南省香格里拉纳帕海国际重要湿地野禽粪样及其周边家禽喉头、泄殖腔和环境水样,经尿囊腔接种10日龄SPF鸡胚分离病毒,结合HA试验和RT-PCR扩增鉴定AIV亚型。利用MBTuni-12/13引物同时扩增H9N2亚型AIV毒株的8个基因(HA、NA、M、PB2、NS、NP、PA及PB1)节段,利用二代测序获取全基因组序列,并分析遗传进化关系及关键氨基酸突变位点。【结果】分离到的4株野鸟源H9N2亚型AIV的HA、NA基因源自Y280-like亚系,M、PB 2基因为G1-like亚系,NS、NP、PA、PB 1基因为F/98-like亚系,表明4株分离株为多种亚型的重组毒株,重组模式与2013年以后在中国流行的G57基因型一致。序列相似性分析结果显示,4株H9N2亚型AIV分离株内部基因与H7N9、H5N6、H5N2等亚型AIV相似性较高,遗传多样性特征突出。HA蛋白裂解位点均符合低致病性禽流感特征,获得了多个可增加跨种感染风险及与哺乳动物致病力增强相关的氨基酸突变位点,包括A198T、Q234L、N166D(HA),I292V、A558V(PB2),I368V、L13P(PB1),N30D、T215A(M1),以及P42S(NS1)等。4株野鸟源H9N2亚型AIV毒株具有家禽源同亚型毒株特征,野禽源AIV可能源于家禽。【结论】从云南纳帕海国际重要湿地分离到的4株野鸟源H9N2亚型AIV可能是由家禽传播的多源重配病毒,属于G57基因型,且具有多个适应哺乳动物宿主相关的氨基酸突变位点。

基于宏基因组学的野生鸟类肠道菌群研究现状

肠道微生物对鸟类宿主至关重要,宏基因组学技术是研究野生鸟类肠道菌群的重要手段,且研究方法已较为成熟。本文对宏基因组技术在野生鸟类肠道菌群的发展现状进行了总结,并结合其在野生鸟类肠道微生物领域中的具体应用,对野生鸟类肠道微生物的组成、影响因素及肠道微生物功能进行了梳理,以期为野生鸟类尤其是濒危鸟类的保护研究提供新的方向,进一步推动宏基因组学在野生鸟类肠道菌群研究中的应用。

野鸟源禽副黏病毒的流行病学调查及遗传进化分析

目的:调查我国野生鸟类中禽副黏病毒(Avian Paramyxoviruses,APMV)的流行和进化趋势。方法:通过RT-PCR、鸡胚分毒、血凝试验、遗传进化分析对野鸟源样品进行APMV流行病学调查和进化分析。结果:1219份野鸟样品中共检测出9份APMV阳性样品,APMV感染率为0.74%。其中APMV-1有8份,感染率为0.66%;APMV-4有1份,感染率为0.08%。鸡胚分毒成功分离出1株鸽源PPMV-1,遗传进化分析显示其属于基因VI.2.1.1.2.2型,与近年来国内流行的基因型一致。结论:野鸟在APMV的传播中具有重要作用,应加强对野鸟源PPMV-1的监测,研究结果对可能因跨种传播导致的公共卫生事件进行早期预警防控提供理论依据。

Avian influenza virus surveillance in migratory birds in Egypt revealed a novel reassortant H6N2 subtype

Background:Avian influenza viruses(AIVs)have been identified from more than 100 different species of wild birds around the globe.Wild migratory birds can act as potential spreaders for AIVs to domestic birds between different countries.Egypt is situated on important migratory flyways for wild birds between different continents.While much is known about circulation of zoonotic potential H5N1 and H9N2 AIVs in domestic poultry in Egypt,little is known about the pivotal role of migratory birds in the maintenance and transmission of the viruses in Egypt.Methods:Targeted AIV surveillance has been conducted in 2017 in different wetlands areas in Northern and Eastern Egypt.Results:AIV of subtype H5 was detected in two bird species.In addition,a novel reassortant strain of the H6N2 subtype was identified which reveals the continuous risk of new influenza virus(es)introduction into Egypt.This novel virus possesses a reassortant pattern originating from different AIV gene pools.Conclusions:Intervention control strategies should be performed to minimize the possible contact of domestic birds with wild birds to lower the risk of virus transmission at this interface.In addition,constant monitoring of AIVs in migratory birds is essential in the early detection of influenza virus introduction into Egypt.

从化无规定马属动物疫病区及缓冲区鸟类多样性研究

为摸清广东从化无规定马属动物疫病区内野生鸟类分布、种群特点、活动规律和迁徙规律,2021年9月至2022年8月,采用样线法对广东从化无规定马属动物疫病区及缓冲区(以广州市从化区为核心的9个区县)进行4个季度、为期1年的野生鸟类多样性调查。共记录记录鸟类146种,隶属于16目51科;其中优势物种为暗绿绣眼鸟Zosterops simplex、红耳鹎Pycnonotus jocosus、白头鹎Pycnonotus sinensis、栗背短脚鹎Hemixos castanonotus、八哥Acridotheres cristatellus、金腰燕Cecropis daurica和黑短脚鹎Hypsipetes leucocephalus。在居留型组成方面,留鸟占总种数的65.1%,冬候鸟占21.9%,夏候鸟占9.6%。在区系组成上,东洋界占68.5%,古北界占21.2%,广布种占10.3%。记录到国家Ⅱ级重点保护鸟类17种,省级重点保护鸟类23种,列入濒危野生动植物种国际贸易公约(CITES)的9种。从化区和增城区的种群数量明显高于其他7个区县;聚类分析表明,从化区与增城区的鸟类物种相似性更高。