Delimiting species boundaries within Dermanyssus Dugès, 1834 (Acari:Dermanyssidae) using a total evidence approach

The genus Dermanyssus is currently composed of 24 hematophagous mite species and includes the Poultry Red Mite, Dermanyssus gallinae, a serious pest in poultry houses. Morphologically, Dermanyssus species fall into two groups corresponding to Moss’ gallinae-group and to hirsutus-group + Microdermanyssus. Species of the gallinae-group exhibit high levels of morphological variability, and are nearly impossible to distinguish. Species of the second group display consistent characters and host associations and are easily distinguishable. Species of the gallinae-group tend to be the major problems in poultry houses and it is unknown whether D. gallinae is the only pest, or if there are numerous cryptic species present in the system.Twenty species of Dermanyssus were tested phylogenetically based on 46 morphological characters. A subset of species, mainly of the gallinae-group, represented each by several populations, was sequenced for two mitochondrial and one nuclear gene regions. This allowed testing their specific status and their interrelationships based and on morphological and molecular characters. The molecular data was analysed separately and in combination with morphological characters. As expected, morphology did a poor job resolving relationships.Molecular data proved more informative. The resulting phylogenetic hypotheses brought some information about interrelationships among species of the gallinae-group showing a split into two main clades. The invasion of human managed environments seems to occur only in taxa within one of the two clades. The host spectrum seems to get enlarged in more derived taxa in the same clade. A delineation of six species within the gallinae-group is provided. Additionally, a key for morphological identification of these species is provided. D. gallinae appears to be the only pest in poultry houses, but is composed of several different and more or less strongly isolated lineages. A new species found from the black swift is described.     

Variation in chemical composition and acaricidal activity against Dermanyssus gallinae of four eucalyptus essential oils

The results of this study suggest that certain eucalyptus essential oils may be of use as an alternative to synthetic acaricides in the management of the poultry red mite, Dermanyssus gallinae. At a level of 0.21 mg/cm², the essential oil from Eucalyptus citriodora achieved 85% mortality in D. gallinae over a 24 h exposure period in contact toxicity tests. A further two essential oils from different eucalyptus species, namely E. globulus and E. radiata, provided significantly (P < 0.05) lower mite mortality (11 and 19%, respectively). Notable differences were found between the eucalyptus essential oils regarding their chemical compositions. There appeared to be a trend whereby the essential oils that were composed of the fewer chemical components were the least lethal to D. gallinae. It may therefore be the case that the complexity of an essential oil’s chemical make up plays an important role in dictating the toxicity of that oil to pests such as D. gallinae.     

Molecular characterization and phylogenetic inferences of Dermanyssus gallinae isolates in Italy within an European framework

In order to investigate the genetic relationships between Dermanyssus gallinae (Metastigmata: Dermanyssidae) (de Geer) isolates from poultry farms in Italy and other European countries, phylogenetic analysis was performed using a portion of the cytochrome c oxidase subunit 1 (cox1) gene of the mitochondrial DNA and the internal transcribed spacers (ITS1+5.8S+ITS2) of the ribosomal DNA. A total of 360 cox1 sequences and 360 ITS+ sequences were obtained from mites collected on 24 different poultry farms in 10 different regions of Northern and Southern Italy. Phylogenetic analysis of the cox1 sequences resulted in the clustering of two groups (A and B), whereas phylogenetic analysis of the ITS+ resulted in largely unresolved clusters. Knowledge of the genetic make‐up of mite populations within countries, together with comparative analyses of D. gallinae isolates from different countries, will provide better understanding of the population dynamics of D. gallinae. This will also allow the identification of genetic markers of emerging acaricide resistance and the development of alternative strategies for the prevention and treatment of infestations.     

Molecular characterization of the Fe‑hydrogenase gene marker in Trichomonas gallinae isolated from birds in Riyadh,Saudi Arabia

Trichomonas gallinae causes avian oropharyngeal trichomonosis. This pathogen affects a large number of bird species and may cause substantial economic losses to the poultry industry. Al-Azizia poultry market in Riyadh, Saudi Arabia is among the largest poultry markets in the Arabian Gulf. Birds traded in this market may be exposed to a variety of T. gallinae strains. Genetic diversity of T. gallinae among birds in the market was examined using Fe‑hydrogenase gene sequences. These sequences were amplified by PCR for twenty-nine isolates of T. gallinae from four different avian species, including 21 feral pigeons, one common mynah, three chickens, and four turkeys. Sequence analysis showed ten variant gene sequences. Nine sequences comprise a new subtype, including A(KSAF1), C(KSAF1) and C(KSAF3) with 34.48% (n = 10), 6.90% (n = 2), 6.90% (n = 2) of the isolates, respectively. Analyses also showed an additional five new sequences (KSAF1.1., KSAF2, KSAF13, KSAF14, KSAF15), representing 17.24% of the isolates. Subtype II (KSAF) was found in four feral pigeons (13.80%). To our knowledge, this report is the first to describe genotypes of T. gallinae from pigeons in Saudi Arabia using Fe‑hydrogenase gene sequences for subtyping. Subtype analysis infers the presence of multiple genotypes of T. gallinae in Saudi avian populations.     

Mesostigmatic mites associated with birds and mammals in Iran. A review

There are diverse relationships between mites and birds or mammals. These mites may play an important role in epizootics and in the perpetuation of some significant diseases. The purpose of this study is to revise the current knowledge of mesostigmatic mites occurring on birds, including their nests and mammals and their substrates, in Iran and to compare the results with other regions of the Palearctic ecozone. This study presents a revised list of 38 species of mesostigmatic mite occuring on birds (17 species) and mammals (24 species) or in their nests/substrates in Iran. Dermanyssus gallinae, Ornithonyssus sylviarum and Parasitus hyalinus were found on both birds and mammals. The species composition of mites reported in Iran was compared with other regions of the Palearctic ecozone. Parasites, specifically those from genera Dermanyssus, Ornithonyssus and Liponyssoides, may be hazardous to human health. Species from these genera were predominant among the reported mites.     

The poultry red mite (Dermanyssus gallinae): a potential vector of pathogenic agents

The poultry red mite, D. gallinae has been involved in the transmission of many pathogenic agents, responsible for serious diseases both in animals and humans. Nowadays, few effective methods are available to control the ectoparasite in poultry farms. Consequently, this is an emerging problem which must be taken into account to maintain good health in commercial egg production. This paper addresses the vector capacity of the ectoparasite with special emphasis on salmonellae, pathogenic agents responsible for many of the most important outbreaks of food-borne diseases worlwide. It has been experimentally shown that D. gallinae could act as a biological vector of S. enteritidis and natural carriage of these bacteria by the mite on poultry premises has also been reported. It was also found that D. gallinae carried other pathogens such as E. coli, Shigella sp., and Staphylococcus, thus increasing the list of pathogenic agents potentially transmitted by the mite.     

Risk Factors for Infectious Diseases in Backyard Poultry Farms in the Poyang Lake Area,China

Emergence and transmission of infectious diseases have an enormous impact on the poultry industry and present a serious threat to the health of humans and wild birds. Noncommercial poultry operations, such as backyard poultry facilities in China, are potential sources of virus exchange between commercial poultry and wild birds. It is particularly critical in wetland areas where backyard poultry have close contact with commercial poultry and migratory birds, therefore increasing the risk of contracting infectious diseases. To evaluate the transmission risks, a cross-sectional study was undertaken in the Poyang Lake area, China, involving 309 residents in the backyard poultry farms in three counties (Region A, B, and C) of Jiangxi Province. We examined the backyard poultry population, poultry species, presence of poultry deaths from infectious diseases, food sources, and biosecurity practices. Region B ranked highest for biosecurity while region C ranked lowest. The risks of infectious diseases were assessed by adjusted odds ratio based on multivariate logistic regression analysis. Potential risk factors in the three regions of the study site were compared. In Region A, significant factor was contact of poultry with wild birds (OR: 6.573, 95% CI: 2.148–20.115, P=0.001). In Region B, the most significant factor was contact of poultry with neighboring backyard waterfowls (OR: 3.967, 95% CI: 1.555–10.122, P=0.004). In Region C, significant factors were poultry purchase from local live bird markets (OR: 3.740, 95% CI: 1.243–11.255, P=0.019), and contact of poultry with wild birds (OR: 3.379, 95% CI: 1.058–10.791, P=0.040). In summary, backyard poultry was significantly affected by neighboring commercial poultry and close contact with wild birds. The results are expected to improve our understanding of the transmission risks of infectious diseases in a typical backyard poultry environment in rural China, and address the need to improve local farming practices and take preventive measures.     

Diverse Wild Bird Host Range of Mycoplasma gallisepticum in Eastern North America

Emerging infectious diseases often result from pathogens jumping to novel hosts. Identifying possibilities and constraints on host transfer is therefore an important facet of research in disease ecology. Host transfers can be studied for the bacterium Mycoplasma gallisepticum, predominantly a pathogen of poultry until its 1994 appearance and subsequent epidemic spread in a wild songbird, the house finch Haemorhous mexicanus and some other wild birds. We screened a broad range of potential host species for evidence of infection by M. gallisepticum in order to answer 3 questions: (1) is there a host phylogenetic constraint on the likelihood of host infection (house finches compared to other bird species); (2) does opportunity for close proximity (visiting bird feeders) increase the likelihood of a potential host being infected; and (3) is there seasonal variation in opportunity for host jumping (winter resident versus summer resident species). We tested for pathogen exposure both by using PCR to test for the presence of M. gallisepticum DNA and by rapid plate agglutination to test for the presence of antibodies. We examined 1,941 individual birds of 53 species from 19 avian families. In 27 species (15 families) there was evidence for exposure with M. gallisepticum although conjunctivitis was very rare in non-finches. There was no difference in detection rate between summer and winter residents, nor between feeder birds and species that do not come to feeders. Evidence of M. gallisepticum infection was found in all species for which at least 20 individuals had been sampled. Combining the present results with those of previous studies shows that a diverse range of wild bird species may carry or have been exposed to M. gallisepticum in the USA as well as in Europe and Asia.     

Emerging Infectious Disease Leads to Rapid Population Declines of Common British Birds

Emerging infectious diseases are increasingly cited as threats to wildlife, livestock and humans alike. They can threaten geographically isolated or critically endangered wildlife populations; however, relatively few studies have clearly demonstrated the extent to which emerging diseases can impact populations of common wildlife species. Here, we report the impact of an emerging protozoal disease on British populations of greenfinch Carduelis chloris and chaffinch Fringilla coelebs, two of the most common birds in Britain. Morphological and molecular analyses showed this to be due to Trichomonas gallinae. Trichomonosis emerged as a novel fatal disease of finches in Britain in 2005 and rapidly became epidemic within greenfinch, and to a lesser extent chaffinch, populations in 2006. By 2007, breeding populations of greenfinches and chaffinches in the geographic region of highest disease incidence had decreased by 35% and 21% respectively, representing mortality in excess of half a million birds. In contrast, declines were less pronounced or absent in these species in regions where the disease was found in intermediate or low incidence. Also, populations of dunnock Prunella modularis, which similarly feeds in gardens, but in which T. gallinae was rarely recorded, did not decline. This is the first trichomonosis epidemic reported in the scientific literature to negatively impact populations of free-ranging non-columbiform species, and such levels of mortality and decline due to an emerging infectious disease are unprecedented in British wild bird populations. This disease emergence event demonstrates the potential for a protozoan parasite to jump avian host taxonomic groups with dramatic effect over a short time period.     

Arthropods (Acarina, Coleoptera, Siphonaptera) in nests of hoopoe (Upupa epops) in Central Europe

In 1993–1995 and 2009–2011, during investigation of reproduction biology of hoopoe, 63 nests of this species were collected after fledging of the chicks in Slovakia and Austria and their arthropod fauna was analyzed. Altogether 5,481 individuals and 34 species of mesostigmatic mites were found in 82.5% of the nests examined. The nidicolous mite Androlaelaps casalis was most abundant and frequent, representing 91.7% of all individuals. The richest in species were saprophilous mites (64.7% of all recorded species), while ectoparasites of the genera Dermanyssus and Ornithonyssus represented only 0.4% of all mites. Only 8 beetle species represented by 65 individuals were found in 18 nests. The dominant trophical group were carnivores (mainly nidicolous Gnathoncus buyssoni) with almost identical representation in (86.2%), followed by a similar representation of necrophags (10.8%). Unlike nests of other birds, the typical nidicolous species Haploglossa puncticollis and the fungivors were absent due to the dry character of studied countryside and placement of the nests in boxes situated in vineyard cottages. Only one species of fleas, Ceratophyllus gallinae — parasitizing first of all in the passeriform birds and being particularly abundant in the cavity nesting birds was recorded in hoopoe nests.     

Monitoring exposure to avian influenza viruses in wild mammals

• 1 Avian influenza (AI) viruses primarily circulate in wild waterfowl populations and are occasionally transmitted to domestic poultry flocks. However, the possible roles of other wildlife species, such as wild mammals, in AI virus ecology have not been adequately addressed.
• 2 Due to their habitat and behaviour, many wild mammals may be capable of transmitting pathogens among wild and domestic populations. Exposure to AI viruses has been reported in an array of wild and domestic animals. The presence of wild mammals on farms has been identified as a risk factor for at least one poultry AI outbreak in North America. These reports suggest the need for seroprevalence studies examining the exposure of wild mammals to AI viruses.
• 3 Serological tests are routinely used to assess domestic poultry, domestic swine and human exposure to influenza A viruses, but these tests have not been validated for use in wild mammals. As such, some of these protocols may require adjustments or may be inappropriate for use in serology testing of wild mammals. Herein, we review these serological techniques and evaluate their potential usefulness in AI surveillance of wild mammals. We call for care to be taken when applying serological tests outside their original area of validation, and for continued assay verification for multiple species and virus strains.

     

Candidate predators for biological control of the poultry red mite Dermanyssus gallinae

The poultry red mite, Dermanyssus gallinae, is currently a significant pest in the poultry industry in Europe. Biological control by the introduction of predatory mites is one of the various options for controlling poultry red mites. Here, we present the first results of an attempt to identify potential predators by surveying the mite fauna of European starling (Sturnus vulgaris) nests, by assessing their ability to feed on poultry red mites and by testing for their inability to extract blood from bird hosts, i.e., newly hatched, young starlings and chickens. Two genuine predators of poultry red mites are identified: Hypoaspis aculeifer and Androlaelaps casalis. A review of the literature shows that some authors suspected the latter species to parasitize on the blood of birds and mammals, but they did not provide experimental evidence for these feeding habits and/or overlooked published evidence showing the reverse. We advocate careful analysis of the trophic structure of arthropods inhabiting bird nests as a basis for identifying candidate predators for control of poultry red mites.     

Using mitochondrial and nuclear sequence data for disentangling population structure in complex pest species: a case study with Dermanyssus gallinae

Among global changes induced by human activities, association of breakdown of geographical barriers and impoverishered biodiversity of agroecosystems may have a strong evolutionary impact on pest species. As a consequence of trade networks' expansion, secondary contacts between incipient species, if hybrid incompatibility is not yet reached, may result in hybrid swarms, even more when empty niches are available as usual in crop fields and farms. By providing important sources of genetic novelty for organisms to adapt in changing environments, hybridization may be strongly involved in the emergence of invasive populations. Because national and international trade networks offered multiple hybridization opportunities during the previous and current centuries, population structure of many pest species is expected to be the most intricate and its inference often blurred when using fast-evolving markers. Here we show that mito-nuclear sequence datasets may be the most helpful in disentangling successive layers of admixture in the composition of pest populations. As a model we used D. gallinae s. l., a mesostigmatid mite complex of two species primarily parasitizing birds, namely D. gallinae L1 and D. gallinae s. str. The latter is a pest species, considered invading layer farms in Brazil. The structure of the pest as represented by isolates from both wild and domestic birds, from European (with a focus on France), Australian and Brazilian farms, revealed past hybridization events and very recent contact between deeply divergent lineages. The role of wild birds in the dissemination of mites appears to be null in European and Australian farms, but not in Brazilian ones. In French farms, some recent secondary contact is obviously consecutive to trade flows. Scenarios of populations' history were established, showing five different combinations of more or less dramatic bottlenecks and founder events, nearly interspecific hybridizations and recent population mixing within D. gallinae s. str.     

High Prevalence of West Nile Virus in Domestic Birds and Detection in 2 New Mosquito Species in Madagascar

West Nile virus is an arthropod-borne zoonosis transmitted by a large number of mosquito species, and birds play a key role as reservoir of the virus. Its distribution is largely widespread over Africa, Asia, the Americas and Europe. Since 1978, it has frequently been reported in Madagascar. Studies described a high seroprevalence level of the virus in humans in different areas of the island and a human fatal case of WNV infection was reported in 2011. Despite these reports, the epidemiology of WNV in Madagascar, in particular, viral circulation remains unclear. To explore the transmission of WNV in two rural human populations of Madagascar, we investigated local mosquitoes and poultry for evidence of current infections, and determined seroprevalence of candidate sentinel species among the local poultry. These 2 areas are close to lakes where domestic birds, migratory wild birds and humans coexist. Serological analysis revealed WNV antibodies in domestic birds (duck, chicken, goose, turkey and guinea fowl) sampled in both districts (Antsalova 29.4% and Mitsinjo 16.7%). West Nile virus nucleic acid was detected in one chicken and in 8 pools of mosquitoes including 2 mosquito species (Aedeomyia madagascarica and Anopheles pauliani) that have not been previously described as candidate vectors for WNV. Molecular analysis of WNV isolates showed that all viruses detected were part of the lineage 2 that is mainly distributed in Africa, and were most closely matched by the previous Malagasy strains isolated in 1988. Our study showed that WNV circulates in Madagascar amongst domestic birds and mosquitoes, and highlights the utility of poultry as a surveillance tool to detect WNV transmission in a peri-domestic setting.     

Generalist nematodes dominate the nemabiome of roe deer in sympatry with sheep at a regional level

The growth of livestock farming and the recent expansion of wild ungulate populations in Europe favor opportunities for direct and/or indirect cross-transmission of pathogens. Comparatively few studies have investigated the epidemiology of gastro-intestinal nematode parasites, an ubiquitous and important community of parasites of ungulates, at the wildlife/livestock interface. In this study, we aimed to assess the influence of livestock proximity on the gastrointestinal nematode community of roe deer in a rural landscape located in southern France. Using ITS-2 rDNA nemabiome metabarcoding on fecal larvae, we analysed the gastrointestinal nematode communities of roe deer and sheep. In addition, we investigated Haemonchus contortus nad4 mtDNA diversity to specifically test parasite circulation among domestic and wild host populations. The dominant gastrointestinal nematode species found in both the roe deer and sheep were generalist species commonly found in small ruminant livestock (e.g. H. contortus), whereas the more specialised wild cervid nematode species (e.g. Ostertagia leptospicularis) were only present at low frequencies. This is in marked contrast with previous studies that found the nemabiomes of wild cervid populations to be dominated by cervid specialist nematode species. In addition, the lack of genetic structure of the nad4 mtDNA of H. contortus populations between host species suggests circulation of gastrointestinal nematodes between roe deer and sheep. The risk of contact with livestock only has a small influence on the nemabiome of roe deer, suggesting the parasite population of roe deer has been displaced by generalist livestock parasites due to many decades of sheep farming, not only for deer grazing close to pastures, but also at a larger regional scale. We also observed some seasonal variation in the nemabiome composition of roe deer. Overall, our results demonstrate significant exchange of gastrointestinal nematodes between domestic and wild ungulates, with generalist species spilling over from domestic ungulates dominating wild cervid parasite communities.     

Monitoring of Dermanyssus gallinae in free-range poultry farms

Various methods for monitoring Dermanyssus gallinae infestations within free-range egg production units were compared. The study was carried out in five egg-producing free-range poultry buildings infested with D. gallinae. Each farm was divided into six zones (each zone including nest boxes, perches and duckboard) for placing two types of traps (corrugated cardboard and thick card traps) or examining dried droppings for presence of mites. Traps were removed 24 h later, placed into bags and mites were counted at the laboratory using binocular magnification. Droppings were also inspected by eye and mite numbers were estimated. All the methods used allowed us to detect mites although their efficacy differed. The number of mites collected was independent of the type of trap used. Examination of the droppings did not differentiate between buildings with differing mite populations. Placing traps in the nest boxes is a less reliable indicator than placing them on the perches. It appears that the most coherent method for evaluating the D. gallinae population within a free-range flock is to place thick card traps throughout the building, on perches favoured by birds.     

Are Poultry or Wild Birds the Main Reservoirs for Avian Influenza in Bangladesh?

Avian influenza viruses (AIV) are of great socioeconomic and health concern, notably in Southeast Asia where highly pathogenic strains, such as highly pathogenic avian influenza (HPAI) H5N1 and other H5 and H7 AIVs, continue to occur. Wild bird migrants are often implicated in the maintenance and spread of AIV. However, little systematic surveillance of wild birds has been conducted in Southeast Asia to evaluate whether the prevalence of AIV in wild birds is higher than in other parts of the world where HPAI outbreaks occur less frequently. Across Bangladesh, we randomly sampled a total of 3585 wild and domestic birds to assess the prevalence of AIV and antibodies against AIV and compared these with prevalence levels found in other endemic and non-endemic countries. Our study showed that both resident and migratory wild birds in Bangladesh do not have a particularly elevated AIV prevalence and AIV sero-prevalence compared to wild birds from regions in the world where H5N1 is not endemic and fewer AIV outbreaks in poultry occur. Like elsewhere, notably wild birds of the orders Anseriformes were identified as the main wild bird reservoir, although we found exceptionally high sero-prevalence in one representative of the order Passeriformes, the house crow (Corvus splendens), importantly living on offal from live bird markets. This finding, together with high sero- and viral prevalence levels of AIV in domestic birds, suggests that wild birds are not at the base of the perpetuation of AIV problems in the local poultry sector, but may easily become victim to AIV spill back from poultry into some species of wild birds, potentially assisting in further spread of the virus.     

The testing of antibodies raised against poultry red mite antigens in an in vitro feeding assay; preliminary screen for vaccine candidates

Dermanyssus gallinae (De Geer), the poultry red mite, is a blood-feeding ectoparasite that infests many bird species. We have used an in vitro feeding assay to allow the identification of protective D. gallinae antigens that may have potential as vaccine candidates. Homogenised mites were extracted sequentially with PBS, Tween 20, Triton X100 and urea giving four protein fractions. Five experimental groups of Lohmann Brown hens were used to generate antibodies; four groups were injected with one of each of the protein fractions in QuilA adjuvant and a control group was injected with adjuvant only. Booster injections were administered 2 and 4 weeks after initial immunisation. Eggs were collected throughout the experiment and soluble IgY antibodies were extracted from a pool of egg yolks collected at week six post-injection. Western blots, performed using post vaccination antibodies from test and control groups, revealed a strong antibody response against a range of injected proteins. Fresh chicken blood, supplemented with antibodies raised against these protein fractions, was fed to mites in an in vitro feeding assay in order to determine whether the antibodies had an anti-mite effect. Although there was variability in the numbers of feeding mites, it was found that the strongest anti-mite effect was seen with the PBS protein fraction, which had a cumulative average mortality of 34.8% 14 days after feeding compared with 27.3% for the control group (P = 0.043).     

Evidence of infection by H5N2 highly pathogenic avian influenza viruses in healthy wild waterfowl

The potential existence of a wild bird reservoir for highly pathogenic avian influenza (HPAI) has been recently questioned by the spread and the persisting circulation of H5N1 HPAI viruses, responsible for concurrent outbreaks in migratory and domestic birds over Asia, Europe, and Africa. During a large-scale surveillance programme over Eastern Europe, the Middle East, and Africa, we detected avian influenza viruses of H5N2 subtype with a highly pathogenic (HP) viral genotype in healthy birds of two wild waterfowl species sampled in Nigeria. We monitored the survival and regional movements of one of the infected birds through satellite telemetry, providing a rare evidence of a non-lethal natural infection by an HP viral genotype in wild birds. Phylogenetic analysis of the H5N2 viruses revealed close genetic relationships with H5 viruses of low pathogenicity circulating in Eurasian wild and domestic ducks. In addition, genetic analysis did not reveal known gallinaceous poultry adaptive mutations, suggesting that the emergence of HP strains could have taken place in either wild or domestic ducks or in non-gallinaceous species. The presence of coexisting but genetically distinguishable avian influenza viruses with an HP viral genotype in two cohabiting species of wild waterfowl, with evidence of non-lethal infection at least in one species and without evidence of prior extensive circulation of the virus in domestic poultry, suggest that some strains with a potential high pathogenicity for poultry could be maintained in a community of wild waterfowl.     

High Levels of Antimicrobial Resistance among Escherichia coli Isolates from Livestock Farms and Synanthropic Rats and Shrews in the Mekong Delta of Vietnam

In Mekong Delta farms (Vietnam), antimicrobials are extensively used, but limited data are available on levels of antimicrobial resistance (AMR) among Escherichia coli isolates. We performed a structured survey of AMR in E. coli isolates (n = 434) from 90 pig, chicken, and duck farms. The results were compared with AMR among E. coli isolates (n = 234) from 66 small wild animals (rats and shrews) trapped on farms and in forests and rice fields. The isolates were susceptibility tested against eight antimicrobials. E. coli isolates from farmed animals were resistant to a median of 4 (interquartile range [IQR], 3 to 6) antimicrobials versus 1 (IQR, 1 to 2) among wild mammal isolates (P < 0.001). The prevalences of AMR among farmed species isolates (versus wild animals) were as follows: tetracycline, 84.7% (versus 25.6%); ampicillin, 78.9% (versus 85.9%); trimethoprim-sulfamethoxazole, 52.1% (versus 18.8%); chloramphenicol, 39.9% (versus 22.5%); amoxicillin-clavulanic acid, 36.6% (versus 34.5%); and ciprofloxacin, 24.9% (versus 7.3%). The prevalence of multidrug resistance (MDR) (resistance against three or more antimicrobial classes) among pig isolates was 86.7% compared to 66.9 to 72.7% among poultry isolates. After adjusting for host species, MDR was ∼8 times greater among isolates from wild mammals trapped on farms than among those trapped in forests/rice fields (P < 0.001). Isolates were assigned to unique profiles representing their combinations of susceptibility results. Multivariable analysis of variance indicated that AMR profiles from wild mammals trapped on farms and those from domestic animals were more alike (R² range, 0.14 to 0.30) than E. coli isolates from domestic animals and mammals trapped in the wild (R² range, 0.25 to 0.45). The results strongly suggest that AMR on farms is a key driver of environmental AMR in the Mekong Delta.