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）,

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.

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.

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.

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.

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 .

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.

The Evidence of Clade 7.1 Avian Influenza Virus (H5N1) in Qinghai Lake

The highly pathogenic influenza A virus subtype H5N1 spread throughout Asia since 2003, reached to Europe in 2005, and the Middle East, as well as Africa and caused a global concern for a potential pandemic threat last decade. A Clade 2.3.2 H5N1 virus became dominate in the Qinghai Lake region in 2009 with sporadic mammal cases of infection and transferred to Russia and Europe through wild migratory birds. Currently, HPAI H5N1 of clades 2.3.4, 2.3.2, and 7 are the dominant co-circulating H5N1 viruses in poultry in Asia. 2.3.2 Clade is dominant in wild birds through the world whereas there is no evident data about Clade 7 circulation in wild birds. We detected HPAI H5N1 virus of Clade 7.1 in Qinghai Lake, that closely related to Shanxi-like and Vietnam viruses co-circulating in poultry. This is the first report of Clade 7.1 H5N1 in wild birds. Based on phylogenetic analyses, the virus can be originated from Clade 7.1 virus gene pool that spread in Vietnam and Chinese poultry and could spread with migratory birds to Qinghai Lake. The Qinghai Lake continues to be significant hotspot for H5N1 surveillance since the regular outbreaks occurred there in wild birds and mammals. Based on these facts and findings, the related researchers should pay more attention to the Qinghai Lake basin as significant hotspot for H5N1 avian influenza surveillance since the regular H5N1 outbreaks occurred there in wild birds with sporadic mammal cases of infection.

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.