Bird Feces Research Articles

Circulation of avian Chlamydia abortus in the Netherlands and community-acquired pneumonia: an outbreak investigation and retrospective cohort study

In 2021, a novel group of Chlamydia strains in wild birds was classified as avian Chlamydia abortus, with unknown zoonotic potential. We report relevant features of avian C abortus infections from a Dutch family cluster and unrelated historical cases using clinical, epidemiological, and microbiological data. An outbreak of avian C abortus started in the Netherlands in December, 2022. Source investigation was done using questionnaires to interview patients and environmental sampling. The outbreak strain of avian C abortus was cultured from three patients from whom sufficient material was available for culture and underwent whole-genome analysis. The outbreak strains and retrospective cohort study strains previously submitted to the National Human Psittacosis surveillance programme in the Netherlands between 2010 and 2022 were typed by partial ompA sequencing. Strains with the same aberrant ompA genotype were further analysed with XerC gene plasmid analysis and compared with closely related Chlamydia sequences available in GenBank. An avian C abortus strain caused a cluster of respiratory illness in four family members. Three patients were hospitalised with community-acquired pneumonia, one of whom was admitted to the intensive care unit. The faeces of wild birds were considered a probable source for the index infection. For two family members, human-to-human transmission was a plausible route. Ten historical cases could be identified with avian C abortus with the same ompA genotype. All patients had been admitted to hospital, at least five developed pneumonia, and one died. This cluster supports that avian C abortus strains can cause human infections and underlines that human-to-human transmission should be considered when tracing the source of such infections. National Institute for Public Health and the Environment and Dutch Ministry of Agriculture, Fisheries, Food Security and Nature. For the Dutch translation of the abstract see Supplementary Materials section.

Molecular Survey of Microsporidia, Blastocystis, Cryptosporidium and Giardia in Pet Avian Species in Tehran, Iran

Background: Opportunistic microorganisms of the intestinal tract, such as Cryptosporidium spp. Giardia spp. Blastocystis sp. and microsporidia, are increasingly responsible for clinical disorders in various host species, including humans. Objectives: This study was conducted to search for the above parasites in the feces of pet birds using parasitological and molecular methods in Tehran City, Iran. Methods: In the current study, fecal samples of avian birds were collected and investigated with modified Ziehl-Neelsen, modified trichrome, and trichrome staining for the presence of microsporidia, Cryptosporidium, Blastocystis and Giardia. All the samples were examined molecularly with specific primers and PCR methods. Results: Three of the examined droppings contained Encephalitozoon hellem genotype 1B (2%) by PCR and sequencing. The microsporidian organisms were recovered from the droppings of a clinically normal green-cheek parakeet, an African gray parrot, and a lovebird. Other parasites that were examined were not found in the analyzed samples. Conclusion: The current study proved that captive pet birds are a possible source of microsporidian infection. Besides the fact that encephalitozoonosis is predominantly subclinical in birds, the highly resistant nature of the microsporidia spores can put the owners at increased risk of disease acquisition via spore inhalation or ingestion.

Year-round monitoring of antibiotic-resistant bacteria in pristine uppermost stream and estimation of pollution sources

Studies on the conditions and pollution routes of antibiotic-resistant bacteria (ARB) in rivers can help provide countermeasures against the spread of ARB. This study focused on the pristine uppermost stream of a river, where Escherichia coli (E. coli) and enterococci were detected, although the stream flows through a pristine forest catchment. Antibiotic resistance of E. coli and enterococci isolated from the river water, riverbed sediment, and feces of waterside animals, such as birds and Mustelidae, were investigated throughout the year in the pristine uppermost sites. Antibiotic resistance was present in 1.4% (7/494) of the E. coli strains and 3.0% (24/812) of the enterococcal strains, and was low throughout the year. Although antibiotic resistance of bacteria isolated from feces was not detected in this watershed, the prevalence of multidrug-resistant E. coli was 0.4% (1/246) and 0.6% (1/172) in river water and riverbed sediment samples, respectively were observed. The presence of extended-spectrum β-lactamase (ESBL)-producing E. coli was confirmed in river water samples, and genomic analysis revealed that the samples possessed the CTX-M-15 group. Multidrug-resistant strains and ESBL-producing strains were classified as phylogroups B1 and A, respectively, which are E. coli phenotypes isolated from wild animals. Pulsed-field gel electrophoresis revealed analysis targeting enterococci that strains isolated from river water and bird feces were in the same cluster with 100% similarity. Therefore, bird feces are a source of enterococci in the uppermost stream of the river. Because multidrug-resistant bacteria and ESBL-producing bacteria were present in the pristine uppermost stream of the pristine river, urgent elucidation of the spreading routes of ARB is important.

Diversity of Culturable Yeasts in the Feces of Mew Gulls Breeding in Natural and Urban Habitats, with Insights into the Antifungal Susceptibility of the Observed Pathogens

Migratory birds play an important role in the spread of yeasts in the environment over long distances and in different geographical regions. Human activities, in turn, have a major impact on the biology of wild birds and, consequently, on the microbial communities for which birds act as carriers and disseminators. We sought to assess the “response” of the diversity of culturable yeasts in the feces of Mew Gulls to the type of nesting site (natural/anthropogenic) during the breeding season from April to October 2023. We isolated and molecularly identified 26 yeast species. The species composition in the feces of birds from the natural habitat was more diverse, and the diversity increased from April to October. In contrast, the diversity in the feces of birds from the urban habitat decreased from April to October. Analysis of susceptibility to conventional antibiotics (fluconazole, voriconazole, and amphotericin B) using the CLSI BMD (Clinical and Laboratory Standards Institute broth microdilution) method in isolated strains of opportunistic Candida (C. parapsilosis and C. tropicalis) and strains of the emerging pathogen Rhodotorula mucilaginosa showed that the proportion of resistant strains was higher in strains isolated from the feces of birds from the anthropogenic population. Mew Gulls that spent their breeding season near a landfill and flew away for wintering appear to be a source for the spread of pathogenic yeasts with resistance against antifungal agents.

Variability of faecal microbiota and antibiotic resistance genes in flocks of migratory gulls and comparison with the surrounding environment

Gulls commonly rely on human-generated waste as their primary food source, contributing to the spread of antibiotic-resistant bacteria and their resistance genes, both locally and globally. Our understanding of this process remains incomplete, particularly in relation to its potential interaction with surrounding soil and water. We studied the lesser black-backed gull, Larus fuscus, as a model to examine the spatial variation of faecal bacterial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) and its relationship with the surrounding water and soil. We conducted sampling campaigns within a connectivity network of different flocks of gulls moving across functional units (FUs), each of which represents a module of highly interconnected patches of habitats used for roosting and feeding. The FUs vary in habitat use, with some gulls using more polluted sites (notably landfills), while others prefer more natural environments (e.g., wetlands or beaches). Faecal bacterial communities in gulls from flocks that visit and spend more time in landfills exhibited higher richness and diversity. The faecal microbiota showed a high compositional overlap with bacterial communities in soil. The overlap was greater when compared to landfill (11%) than to wetland soils (6%), and much lower when compared to bacterial communities in surrounding water (2% and 1% for landfill and wetland water, respectively). The relative abundance of ARGs and MGEs were similar between FUs, with variations observed only for specific families of ARGs and MGEs. When exploring the faecal carriage of ARGs and MGEs in bird faeces relative to soil and water compartments, gull faeces were enriched in ARGs classified as High-Risk. Our results shed light on the complex dynamics of antibiotic resistance spread in wild bird populations, providing insights into the interactions among gull movement and feeding behavior, habitat characteristics, and the dissemination of antibiotic resistance determinants across environmental reservoirs.

Ungrazed seminatural habitats around farms benefit bird conservation without enhancing foodborne pathogen risks

ContextConservation in working landscapes is critical for halting biodiversity declines and ensuring farming system sustainability. However, concerns that wildlife may carry foodborne pathogens has created pressure on farmers to remove habitat and reduce biodiversity, undermining farmland conservation. Nonetheless, simplified farming landscapes may host bird communities that carry higher foodborne disease risks.ObjectivesWe analyzed the effects of local farming practices and surrounding landscapes on bird communities and food-safety risks across 30 California lettuce farms. Specifically, we sought to determine how farmland diversification affects bird diversity, fecal contamination, and foodborne pathogen incidences, thereby identifying potential tradeoffs between managing farms for bird conservation versus food safety.MethodsWe surveyed birds at 227 point-count locations, quantified fecal contamination along 120 transects, and assayed 601 bird feces for pathogenic E. coli, Campylobacter spp., and Salmonella spp. We then used hierarchical models to quantify effects of farm management and landscape context on bird communities and food-safety risks.ResultsSurrounding ungrazed seminatural areas were associated with higher bird diversity, more species of conservation concern, and fewer flocks that may increase risks from foodborne pathogens. In contrast, on-farm diversification practices and surrounding grazing lands offered weaker bird conservation benefits. Surrounding grazed lands were associated with more potentially pathogenic bird feces in crop fields.ConclusionsOur results suggest that habitat conservation around produce farms could support bird conservation without increasing foodborne pathogens, especially on farms further from grazing lands. Thus, interventions that diversify farming systems offer potential to simultaneously conserve biodiversity and provide safe food for human consumption.

ESBL-Producing Enterobacterales at the Human-Domestic Animal-Wildlife Interface: A One Health Approach to Antimicrobial Resistance in Piauí, Northeastern Brazil.

The use, misuse, and overuse of antimicrobials is one of the main public health threats of the 21st century. We investigated the risk factor of the presence of extended-spectrum, cephalosporin-resistant Enterobacterales in feces of non-domestic and domestic birds and other domestic animals in Piauí State, northeast Brazil. We collected a total of 387 cloacal and rectal swab samples of free-living birds, domestic birds, and domestic mammals in five municipalities: Amarante, Água Branca, Lagoa Alegre, Parnaíba, and Teresina. A total of 59/387 (15.2%) of these samples harbored extended spectrum beta-lactamase (ESBL)-producing Enterobacterales. Using the MALDI-TOF technique, we identified fifty-seven samples as Escherichia coli and two samples as Klebsiella pneumoniae. Teresina and Parnaíba had the highest prevalence of animals with resistant bacteria (32.1% and 27.1%, respectively) and highest exposure risk factor (OR of 16.06 and 8.58, respectively, and p < 0.001 for all). Multidrug-resistant, ESBL-producing Enterobacterales were observed in 72.8% of the samples (43/59). For the free-living birds, the positive samples belonged to a great kiskadee (Pitangus sulphuratus) and a semipalmated sandpiper (Calidris pusilla) in migratory and resident species, respectively. For domestic animals, the swine samples showed the highest prevalence of antimicrobial resistance. The lack of access to veterinary care and information regarding antimicrobial therapy, along with the easy access to antimicrobials without medical prescription, favors the inadequate use of antimicrobials in Piauí.

Surveillance and Genetic Analysis of Low-Pathogenicity Avian Influenza Viruses Isolated from Feces of Wild Birds in Mongolia, 2021 to 2023.

The introduction of novel highly pathogenic (HPAI) viruses into Korea has been attributed to recombination events occurring at breeding sites in the Northern Hemisphere. This has increased interest in monitoring and genetically analyzing avian influenza viruses (AIVs) in northern regions, such as Mongolia, which share migratory bird flyways with Korea. AIVs in Mongolia were monitored by analyzing 10,149 fecal samples freshly collected from wild birds from April to October in 2021 to 2023. The prevalence of AIVs in wild birds was 1.01%, with a total of 77 AIVs isolated during these 3 years. These 77 AIVs included hemagglutinin (HA) subtypes H1, H2, H3, H4, H6, H10 and H13 and neuraminidase (NA) subtypes N1, N2, N3, N6, N7 and N8. The most frequently detected subtype combinations were H3N8 (39.0%) and H4N6 (19.5%), although HPAI viruses were not detected. Genetic analysis indicated that theses AIVs isolated from Mongolian samples were closely related to AIVs in wild birds in Korea, including those of Eurasian lineage. These findings indicate the necessity of continuous AIV surveillance and monitoring, as HPAI viruses introduced into Korea may derive from strains in Mongolia.

A simple Preservation Method of Bird Feces for DNA Analysis: A Case Study on Chicken and Quail

Standardized methods for fecal sample collection and safe long-distance transportation for DNA extraction are yet to be identified. We compared four different preservation methods for bird fecal samples: storage in 75% and 100% ethanol, freezing at −20°C, and immersing in 100% ethanol for 3 weeks followed by drying the samples for more than 60 days and transporting them to another country. Our objectives were to quantify the DNA concentration and amplify a fragment of the gene from each sample successfully using the primers mcb398 and mcb869 through DNA barcoding. Our data showed that the method of sample preservation used affected the DNA concentration and amplification. The best results were achieved when the samples were preserved in 100% ethanol. The samples were then dried for storage prior to further processing. This method is inexpensive and safe for long-distance transportation and at airports.

Analyzing the safety of the parasiticide fungus Mucor circinelloides: first insights on its virulence profile and interactions with the avian gut microbial community.

Parasiticide fungi are considered an accurate, sustainable, and safe solution for the biocontrol of animal gastrointestinal (GI) parasites. This research provides an initial characterization of the virulence of the native parasiticide fungus Mucor circinelloides (FMV-FR1) and an assessment of its impact on birds' gut microbes. The genome of this fungus was sequenced to identify the genes coding for virulence factors. Also, this fungus was checked for the phenotypic expression of proteinase, lecithinase, DNase, gelatinase, hemolysin, and biofilm production. Finally, an in vivo trial was developed based on feeding M. circinelloides spores to laying hens and peacocks three times a week. Bird feces were collected for 3 months, with total genomic DNA being extracted and subjected to long-read 16S and 25S-28S sequencing. Genes coding for an iron permease (FTR1), iron receptors (FOB1 and FOB2), ADP-ribosylation factors (ARFs) (ARF2 and ARF6), and a GTPase (CDC42) were identified in this M. circinelloides genome. Also, this fungus was positive only for lecithinase activity. The field trial revealed a fecal microbiome dominated by Firmicutes and Proteobacteria in laying hens, and Firmicutes and Bacteroidetes in peacocks, whereas the fecal mycobiome of both bird species was mainly composed of Ascomycetes and Basidiomycetes fungi. Bacterial and fungal alpha-diversities did not differ between sampling time points after M. circinelloides administrations (P = 0.62 and P = 0.15, respectively). Although findings from this research suggest the lack of virulence of this M. circinelloides parasiticide isolate, more complementary in vitro and in vivo research is needed to conclude about the safety of its administration to birds, aiming at controlling their GI parasites.IMPORTANCEA previous study revealed that the native Mucor circinelloides isolate (FMV-FR1) can develop parasiticide activity toward coccidia oocysts, one of the most pathogenic GI parasites in birds. However, ensuring its safety for birds is of utmost importance, namely by studying its virulence profile and potential effect on commensal gut microbes. This initial study revealed that although this M. circinelloides isolate had genes coding for four types of virulence factors-iron permease, iron receptors, ADP-ribosylation factors, and GTPase-and only expressed phenotypically the enzyme lecithinase, the administration of its spores to laying hens and peacocks did not interfere with the abundances and diversities of their gut commensal bacteria and fungi. Although overall results suggest the lack of virulence of this M. circinelloides isolate, more complementary research is needed to conclude about the safety of its administration to birds in the scope of parasite biocontrol programs.

Virome characterization of diarrheic red-crowned crane (G. japonensis)

BackgroundThe red-crowned crane is one of the vulnerable bird species. Although the captive population has markedly increased over the last decade, infectious diseases can lead to the death of young red-crowned cranes while few virological studies have been conducted.MethodsUsing a viral metagenomics approach, we analyzed the virome of tissues of the dead captive red-crowned crane with diarrhea symptoms in Dongying Biosphere Reserve, Shandong Province, China and feces of individual birds breeding at the corresponding captive breeding center, which were pooled separately.ResultsThere is much more DNA and RNA viruses in the feces than that of the tissues. RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Parvoviridae, associated with enteric diseases were detected in the tissues and feces. Genomes of the picornavirus, genomovirus, and parvovirus identified in the study were fully characterized, which further suggested that infectious viruses of these families were possibly presented in the diseased red-crowned crane.ConclusionRNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Genomoviridae and Parvoviridae were possibly the causative agent for diarrhea of red-crowned crane. This study has expanded our understanding of the virome of red-crowned crane and provides a baseline for elucidating the etiology for diarrhea of the birds.

Coproparasitological research in birds housed at the Sargento Prata Zoo, Fortaleza - Ceará, Brazil.

Birds kept in captivity are subject to various diseases that affect their well-being, with parasites being among the most common. The aim of this study was to report the occurrence of endoparasites in the feces of birds kept in captivity at Fortaleza Zoo, using the Willis Mollay and Hoffman techniques. Of the samples analyzed, 50.98% were positive for endoparasites, including the suborder Coccidia, the genera Capillaria spp., Strongyloides spp., Ascaridia spp., Libyostrongylus spp., cysts of a specific parasite of Ostriches, Balantidium spp., the Strongyloidea superfamily and cestodes. In conclusion, the wild birds in the zoo investigated had a diversity of endoparasites and a considerable infection rate.

Prevalence of Encephalitozoon hellem among companion and exhibition birds in Japan.

Microsporidia can cause infection in various animals and humans. To determine the recent prevalence of Encephalitozoon in companion birds in Japan, 364 bird feces and 16 conjunctival exudates, as well as 28 exhibition bird feces, were examined using polymerase chain reaction (PCR). Thirty-five (9.6%) feces and 2 (12.5%) conjunctival exudates from companion birds were PCR positive, and sequence analysis revealed that all detected organisms were Encephalitozoon hellem genotype 1A. The prevalence by region varied from 4.5% in the Shikoku region to 14.3% in the Chugoku region. By age, the prevalence in birds younger than 6 months of age was 13.3%. We also discuss the threat of human infection as a zoonotic disease.

МОНИТОРИНГ ВОЗБУДИТЕЛЕЙ ОСНОВНЫХ ПАРАЗИТОЗОВ ВОДНЫХ ПТИЦ НА ИЗОЛИРОВАННОЙ ПРИРОДНОЙ ТЕРРИТОРИИ НАЦИОНАЛЬНОГО ПАРКА «ЛОСИНЫЙ ОСТРОВ»

An important point in the conservation of biological diversity and avifauna resources on the territory of national and zoological parks, reserves, as well as commercial breeding poultry enterprises is the study of the bioecology of parasitosis pathogens. In this study, for the first time in a long time, the results of bioecological monitoring of the main parasitoses of aquatic birds living in the isolated natural territory of NP "Losiny оstrov" are presented. The main focus of the work was the study of the spread of the invasive origin in intermediate, additional and final hosts, as well as the conservation potential of aquatic bird species and other components of the biogeocenosis. The article presents the results of helminthological studies of feces of birds of the gull families (lake gull Larus Ridibundus) and duck (mallard Anas Platyrhynchos); helminthological studies of the gastrointestinal tract of fish of the cyprinid family (bream Abramis Brama) and firebrand (perch Perca Fluviatilis); mollusks of the family Lymnaeidae and the family Planorbidae. 85 and 86 individuals of fish and shellfish, respectively, and 116 samples of bird droppings were studied. The number of identified samples from seagulls was 23, from ducks – 47, the remaining 46 samples were defined as «blind samples». The main composition of intestinal parasites of aquatic birds and aquatic organisms has been revealed. Data were obtained on the infection of aquatic birds with associative helminth-protozoal mixinvasion: genera – Eimeria and Trichomonas and helminths of genera: Capillaria, Amidostomum, Heterakis. At the same time, the presence of mixed invasion was noted in 64.28% of the total number of samples. Data were obtained on the infection of fish and shellfish, the helminth fauna of which is represented by the families Echinoctomatidae and Diplostomum sp. The extent of monoinvasion of mollusks of the species Lymnaea stagnalis by cercariae and metacercariae of trematodes of the family Echinoctomatidae was 62.16%.

Metabarcoding reveals waterbird diet in a French Ramsar wetland: implications for ecosystem management

Environmental and/or climate changes, occurring at a global or local scale, can significantly impact the diets, health, and population dynamics of waterbirds. This study aimed to develop an effective tool, using DNA metabarcoding of fecal samples, for monitoring waterbird diets during the breeding season in a Ramsar freshwater wetland in Northern France. We collected bird feces across eight marshes with varying anthropic usage. The majority of samples (69%) were from five waterbird species: Eurasian coot (Fulica atra), Eurasian moorhen (Gallinula chloropus), mallard (Anas platyrhynchos), mute swan (Cygnus olor), and grey heron (Ardea cinerea). DNA was extracted from 116 samples, with plant and invertebrate primers used to undertake multi-marker metabarcoding. Despite a negative impact of uric acid on DNA amplification, we observed significant dietary variations among bird species and sampling sites. Wetland bird diets primarily consisted of four arthropod families, dominated by Chironomidae and Asellidae. The number of plant families detected was higher, consisting of 33 families, with Poaceae highly prevalent within wetland bird diets. This study shows that using DNA metabarcoding to explore interactions between waterbirds and trophic resources is a promising approach to assist wetland management and assess the effect of environmental changes.

Diversity of Fecal Indicator Enterococci among Different Hosts: Importance to Water Contamination Source Tracking.

Enterococcus spp. are common bacteria present in the intestinal tracts of animals and are used as fecal indicators in aquatic environments. On the other hand, enterococci are also known as opportunistic pathogens. Elucidating their composition in the intestinal tracts of domestic animals can assist in estimating the sources of fecal contamination in aquatic environments. However, information on the species and composition of enterococci in animal hosts (except humans) is still lacking. In this study, enterococci were isolated from the feces of cattle, pigs, birds, and humans using selective media. Enterococcal species were identified using mass spectrometry technology, and each host was characterized by diversity and cluster analysis. The most dominant species were E. hirae in cattle, E. faecium in birds, and E. faecalis in pigs and humans. Cattle had the highest alpha diversity, with high interindividual and livestock farm diversity. The dominant enterococcal species in pigs and humans were identical, and cluster analysis showed that the majority of the two hosts' species clustered together.

Effects of monensin sodium and live attenuated oocyst vaccine as coccidiosis management programs on productive performance, bone quality and mineral utilisation in broiler chickens

ABSTRACT 1. The following study was conducted to evaluate the influence of coccidiosis vaccine-induced metabolic stress on the utilisation of minerals in broilers. The starter, grower and finisher phase diets, including macro- and micro minerals at the recommended levels for the breed standards, were fed to chickens between 1 and 39 d of age. 2. A total of 486, one-d-old male broilers were randomly distributed into three coccidiosis management programs (CMP) with six replications each. The CMP comprised: monensin sodium (MON), coccidiosis vaccine (VAC), not treated with MON or VAC (CNT). 3. No significant differences between CMP were observed for body weight and weight gain among treatments. When compared to the CNT, the VAC program increased feed intake (P < 0.05) between d 1 to 13 and 14 to 26, while FCR worsened in the latter (P < 0.05) and the former (P = 0.05) periods. 4. For birds in the MON and VAC programs, tibia bone length at d 13 and bone diameter at d 39 were both enhanced (P < 0.05). Meat yield characteristics were comparable among the CMP. 5. Faeces of VAC birds had a lower (P < 0.05) dry matter and ash content than those in CNT program. CMP had no effect on serum or bone mineral concentrations at any point in time. For minerals, Mg, Na, and K faecal excretion was reduced (P < 0.01) as a result of the VAC program at d 13 with a trend at d 26. 6. Compared to the CNT, the VAC program decreased the percentage ratio of drip loss (P = 0.08), water holding capacity (P < 0.01) and cooking loss (P < 0.01) in breast meat. 7. Overall, the results showed that current broiler industry practices are capable of meeting the mineral needs of broilers vaccinated against coccidiosis.

Prevalence and molecular characterization of Salmonella isolated from wild birds in fresh produce environments.

Wild birds pose a difficult food safety risk to manage because they can avoid traditional wildlife mitigation strategies, such as fences. Birds often use agricultural fields and structures as foraging and nesting areas, which can lead to defecation on crops and subsequent transfer of foodborne pathogens. To assess the food safety risk associated with these events, wild bird feces were collected from produce fields across the southeastern United States during the 2021 and 2022 growing seasons. In total 773 fecal samples were collected from 45 farms across Florida, Georgia, South Carolina, and Tennessee, and 2.1% (n = 16) of samples were Salmonella-positive. Importantly, 75% of Salmonella were isolated from moist feces, showing reduced Salmonella viability when feces dry out. 16S microbiome analysis showed that presence of culturable Salmonella in moist feces correlated to a higher proportion of the Enterobacteriaceae family. From the Salmonella-positive samples, 62.5% (10/16) contained multi-serovar Salmonella populations. Overall, 13 serovars were detected, including six most commonly attributed to human illness (Enteriditis, Newport, Typhimurium, Infantis, Saintpaul, and Muenchen). PCR screening identified an additional 59 Salmonella-positive fecal samples, which were distributed across moist (n = 44) and dried feces (n = 15). On-farm point counts and molecular identification from fecal samples identified 57 bird species, including for 10 Salmonella-positive fecal samples. Overall, there was a low prevalence of Salmonella in fecal samples, especially in dried feces, and we found no evidence of Salmonella transmission to proximal foliage or produce. Fecal samples collected in farms close together shared highly related isolates by whole genome sequencing and also had highly similar Salmonella populations with comparable relative frequencies of the same serovars, suggesting the birds acquired Salmonella from a common source.

Host genetic background rather than diet-induced gut microbiota shifts of sympatric black-necked crane, common crane and bar-headed goose

IntroductionGut microbiota of wild birds are affected by many factors, and host genetic background and diet are considered to be two important factors affecting their structure and function.MethodsIn order to clarify how these two factors influence the gut microbiota, this study selected the sympatric and closely related and similar-sized Black-necked Crane (Grus nigricollis) and Common Crane (Grus grus), as well as the distantly related and significantly different-sized Bar-headed Goose (Anser indicus). The fecal samples identified using sanger sequencing as the above three bird species were subjected to high-throughput sequencing of rbcL gene and 16S rRNA gene to identify the feeding types phytophagous food and gut microbiota.ResultsThe results showed significant differences in food diversity between black-necked cranes and Common Cranes, but no significant differences in gut microbiota, Potatoes accounted for approximately 50% of their diets. Bar-headed Geese mainly feed on medicinal plants such as Angelica sinensis, Alternanthera philoxeroides, and Ranunculus repens. Black-necked cranes and Common Cranes, which have a high-starch diet, have a similar degree of enrichment in metabolism and synthesis functions, which is significantly different from Bar-headed Geese with a high-fiber diet. The differences in metabolic pathways among the three bird species are driven by food. The feeding of medicinal plants promotes the health of Bar-headed Geese, indicating that food influences the functional pathways of gut microbiota. Spearman analysis showed that there were few gut microbiota related to food, but almost all metabolic pathways were related to food.ConclusionThe host genetic background is the dominant factor determining the composition of the microbiota. Monitoring the changes in gut microbiota and feeding types of wild birds through bird feces is of great reference value for the conservation of other endangered species.

Sequencing methods for HA and NA genes of avian influenza viruses from wild bird feces using Oxford Nanopore sequencing

We developed a method to determine the sequences of hemagglutinin (HA) and neuraminidase (NA) from RNA extracted directly from wild bird fecal samples, using Nanopore Flongle. We determined the nucleotide sequences and subtypes of HA and NA in 16 and 15 samples respectively, using Flongle. The results of HA and NA subtyping determined by the conventional method were consistent with their subtypes determined by our method, thereby the applicability of this method in the identification of HA and NA subtypes. In addition, the homology between the HA fragments in this and the Sanger methods ranged from 98.5 % to 100 %. Compared with conventional PCR with the Sanger method, this method can easily determine HA and NA subtypes and sequences directly from the fecal samples. It is easier to implement and has lower running costs (USD100$) than other NGS-based methods, making it a useful tool for avian influenza surveillance in wild birds.