Bird Isolates Research Articles

Role of migratory birds as a risk factor for the transmission of multidrug resistant Salmonella enterica and Escherichia coli to broiler poultry farms and its surrounding environment

Multidrug resistance (MDR) considered as global crisis facing poultry industry. Migratory birds play very important role in the dissemination of antimicrobial resistant pathogen during their fly way specially to poultry farms. Therefore, 750 samples from migratory birds and 300 samples from broiler chicken farms and its environment were collected during the winter seasons of five years (2019 to 2023). The samples were subjected to the isolation of Salmonella enterica and Escherichia coli with the detection of antimicrobial resistance (phenotypic and genotypic) with insight to the genetic similarity between the isolates from migratory birds and broiler chickens’ farms. Different members of Enterobacteriaceae were isolated; Salmonella enterica, Escherichia coli, Citrobacter, Enterobacter, Klebsiella, Proteus, Providencia, Serratia, Hafnia. 298 (28.4%) of S. enterica strains belonging to 27 serovars. S. Typhimurium, S. Kentucky, S. Enteritidis and S. Shangani were the common 4 serotypes between migratory birds and farms. Meanwhile, we found 489 (46.6%) isolates of E. coli belonging to 24 serogroups and O91, O128, O26, O125, O55, O103 and O159 were the common 7serogroups between migratory birds and farms samples. The majority of Salmonella (91.6%; 274 out of 298) and E. coli (92%; 450 out of 489) were MDR. The MDRI range of Salmonella and E. coli was 0.08- 1.The genetic similarity between the isolates of migratory birds and broiler chicken farms were detected by ERICPCR and hot map. This study suggests the continuous applications of surveillance programs for migratory birds and biosecurity measures in poultry farms.

Molecular Detection of Infectious Bronchitis Virus in Captive-Bred Houbara Bustards (Chlamydotis undulata).

This article describes the first reported case of infectious bronchitis virus (IBV) in houbara bustards (Chlamydotis undulata) from Saudi Arabia. Infectious bronchitis virus is a highly infectious virus that leads to major economic losses in the poultry industry. It is prevalent globally and causes severe respiratory and reproductive diseases in chickens. Although a wealth of information exists about IBV prevalence and transmission in domestic birds, similar information is lacking for houbara bustards. The major objectives of this research were to investigate whether IBV infections exist among houbara bustards at the National Wildlife Research Center in Taif, Saudi Arabia, and to determine the prevalence of this virus in this bird population. Fifty-eight oropharyngeal and cloacal swabs were gathered from 29 unvaccinated birds without clinical signs between 2017 and 2023. Extraction of complete RNA from the swab samples and reverse transcription-polymerase chain reaction testing were used to identify IBV. The prevalence of IBV in this population was 37.9% (11 of 29; 95% confidence interval, 20.2-55.5%), indicating transmission asymptomatically among captive houbara bustards. This research identified for the first time that houbara bustards were exposed to IBV, and that this exposure is not uncommon. To counter IBV in Saudi Arabia, recommendations include continuous monitoring of the virus, isolation of infected birds, phylogenetic analysis, genotypic identification of the virus in houbara bustard, and development of an effective vaccination.

The genetic consequences of historic climate change on the contemporary population structure of a widespread temperate North American songbird

Studies of widely distributed species can inform our understanding of how past demographic events tied to historic glaciation and ongoing population genetic processes interact to shape contemporaneous patterns of biodiversity at a continental scale. In this study, we used whole-genome resequencing to investigate the current population structure and genetic signatures of past demographic events in the widespread migratory American goldfinch (Spinus tristis). Phylogenetic relationships inferred from whole mitochondrial genomes were poorly resolved. In contrast, a genome-wide panel of > 4.5 million single nucleotide polymorphisms (SNPs) strongly supported the existence of eastern and western populations separated by western mountain ranges and additional population structuring within the western clade. Demographic modeling estimated that the eastern and western populations diverged approximately one million years ago, and both populations experienced subsequent population bottlenecks during the last glacial period. Species distribution models showed a severe contraction of suitable habitat for the American goldfinch during this period, with predicted discontinuities that are consistent with multiple, isolated glacial refugia that coincide with present-day population structure. Low overall genetic differentiation between the eastern and western populations (FST ∼ 0.01) suggests ongoing gene flow accompanied divergence, and individuals with admixed genomic signatures were sampled along a potential contact zone. Nevertheless, outlier SNPs were identified near genes associated with feather color, song, and migratory behavior and provide strong candidates for further study of the mechanisms underlying reproductive isolation and speciation in birds.

Biosecurity level assessment in commercial poultry farms of central Ethiopia

Proper biosecurity practice is crucial in poultry farming to reduce the risk of diseases. A study was conducted in Adama, Ada’a, and Lume districts, central Ethiopia, to assess the biosecurity measures of commercial poultry farms. A total of 51 farms were randomly selected, and their geographical locations were recorded using GPS devices. The biosecurity level of each farm was assessed using an observation checklist and a biosecurity score. The collected data were analyzed using Stata version 16 for binary data, and QGIS version 3.24.1 was used to map the farms. The results of the study showed that the farms were located close together within 5 km square, 3 km square, and 6 km square areas in Ada’a, Lume, and Adama, respectively. The average distance among the farms was 933.8 meters. The majority of the farms were located within 100 meters of residential areas. Only 58.8% of the farms had adequate space between sheds; 60.8% did not have an adequate drainage system. Ninety-eight percent of the farms obtain chicken from certified breeding enterprises; 92.2% provide underground water for their chickens; 80.4% report frequent cleaning and disinfection of farms; and 82.4% disclose vehicle movement control. Nearly one-third (31.4%) of the farms practice isolation of sick birds but keep them within the same shed where healthy birds are kept. The assessment of biosecurity levels of the study farms revealed that 23.5% (n=12) of the farms had a good biosecurity score, while 76.5% (n=39) had a poor score. The biosecurity scores of the farms showed a statistically significant difference among the study districts (p=0.040), with the Lume district having higher biosecurity scores than Adama and Ada’a districts. The age of the farm owners was significantly associated with the biosecurity score (p=0.003); all farms (100%) owned by individuals aged 20 - 39 had good biosecurity scores, and 80% of those farms owned by individuals aged 40 - 59 had good biosecurity. Farms owned by individuals who have previous chicken-rearing experience had better biosecurity scores than those farms owned by non-experienced owners (p<0.001). Among the farms having professional consultants, 57.7% of them had good biosecurity scores, whereas only 12.0% of farms lacking professional consultants had good biosecurity scores (p=0.015). In conclusion, the study revealed that biosecurity measures were not adequately implemented in poultry farms in central Ethiopia. Farm owners, veterinarians, and livestock authorities must collaborate to implement biosecurity measures to minimize the risk of losses and public health.

Characterization of Gallibacterium anatis Isolated from Pathological Processes in Domestic Mammals and Birds in the Czech Republic.

Gallibacterium anatis, recognized as a resident and opportunistic pathogen primarily in poultry, underwent investigation in unwell domestic mammals and birds. The study encompassed the mapping and comparison of G. anatis isolates, evaluation of their genetic diversity, and determination of their susceptibility to antimicrobials. A total of 11,908 clinical samples were analyzed using cultivation methods and MALDI-TOF. Whole-genome sequencing was performed on seven calf isolates and six hen isolates. Among mammals, G. anatis was exclusively detected in 22 young dairy calves, while among domestic birds, it was found in 35 individuals belonging to four species. Pathological observations in calves were predominantly localized in the digestive tract, whereas in birds, multi-organ infections and respiratory system infections were most prevalent. Distinct groups of genes were identified solely in calf isolates, and conversely, those unique to hen isolates were also recognized. Novel alleles in the multilocus sequence typing scheme genes and previously unidentified sequence types were observed in both calf and hen isolates. Antimicrobial susceptibility exhibited variation between bird and calf isolates. Notably, G. anatis isolates from calves exhibited disparities in genotype and phenotype compared to those from hens. Despite these distinctions, G. anatis isolates demonstrated the capability to induce septicemia in both species.

Automating poultry farm management with artificial intelligence: Real-time detection and tracking of broiler chickens for enhanced and efficient health monitoring.

The broiler industry plays a vital role in meeting the growing global demand for poultry meat. However, maintaining the health and well-being of broiler birds is crucial to ensure both optimal productivity and animal welfare. The increasing mortality rate of broiler chickens developed into an unavoidable issue that required attention. The major goal of this research is to monitor individual chickens for early disease identification, which will then allow for prompt isolation and treatment of sick birds, stopping the spread of pathogens and preserving the health of the flock as a whole. With an accuracy of 96%, the chosen model, YOLOv5s (You Only Look Once), performed the best. Based on their age, the algorithm was able to categorise broiler chickens. The model is converted to ONNX (Open Neural Network Exchange) format after custom training, and the centroid tracker is used for real-time tracking. After that, the output data is kept in a MySQL (My Structured Query Language) database for later use. The OpenCV (Open-Source Computer Vision Library) library is used to deploy this model on a local machine. This model seeks to identify the broiler chicken in the video frame, classify them, and maintain track of them using the tracker. Based on their age, the birds are divided into categories. Since most monitoring is required between 1 and 4weeks of age, they are divided into four age groups. The potential application of this model is in the detection of temperature, weight, flock behaviour, etc.

Farm biosecurity practices affecting avian influenza virus circulation in commercial chicken farms in Bangladesh.

Avian influenza virus (AIV) is of major concern to livestock, wildlife, and human health. In many countries in the world, including Bangladesh, AIV is endemic in poultry, requiring improving biosecurity. In Bangladesh, we investigated how variation in biosecurity practices in commercial chicken farms affected their AIV infection status to help guide AIV mitigation strategies. We collected pooled fecal swabs from 225 farms and tested the samples for the AIV matrix gene followed by H5, H7, and H9 subtyping using rRT-PCR. We found that 39.6% of chicken farms were AIV positive, with 13% and 14% being positive for subtypes H5 and H9, respectively. Using a generalized linear mixed effects model, we identified as many as 12 significant AIV risk factors. Two major factors promoting AIV risk that cannot be easily addressed in the short term were farm size and the proximity of the farm to a live bird market. However, the other ten significant determinants of AIV risk can be more readily addressed, of which the most important ones were limiting access by visitors (reducing predicted AIV risk from 42 to 6%), isolation and treatment of sick birds (42 to 7%), prohibiting access of vehicles to poultry sheds (38 to 8%), improving hand hygiene (from 42 to 9%), not sharing farm workers across farms (37 to 8%), and limiting access by wild birds to poultry sheds (37 to 8%). Our findings can be applied to developing practical and cost-effective measures that significantly decrease the prevalence of AIV in chicken farms. Notably, in settings with limited resources, such as Bangladesh, these measures can help governments strengthen biosecurity practices in their poultry industry to limit and possibly prevent the spread of AIV.

Natural Vector of Avian Haemoproteus asymmetricus Parasite and Factors Altering the Spread of Infection.

Avian haemosporidians (Apicomplexa, Haemosporida) are widespread blood protists, often causing severe haemosporidiosis, pathology, or even mortality in their hosts. Migrant birds regularly bring various haemosporidian parasites from wintering grounds to European breeding areas. Some haemosporidian parasites are prevalent in breeding sites and complete their life cycles in temperate climate zones and can be transmitted, but others do not. The factors altering the spread of these haemosporidians are not fully understood. Culicoides biting midges (Diptera: Ceratopogonidae) play an important role in the transmission of worldwide distributed avian haemosporidian parasites belonging to the genus Haemoproteus, but this information is particularly scarce and insufficient. The key factors limiting the spread of these pathogens in temperate climate zones, which we suspect and aim to study, are the absence of susceptible vectors and the ecological isolation of birds from vectors during the breeding period when transmission occurs. The primary objective of this study was to evaluate how the habitats of biting midges and bird breeding sites influence parasite transmission while also seeking to expand our understanding of the natural vectors for these parasites. Biting midges were collected using UV traps on the Curonian Spit, Lithuania, in different habitats, such as woodland and reeds, from May to September. Parous Culicoides females were identified, dissected, and investigated for the presence of Haemoproteus parasites using both microscopy and PCR-based tools. Among the dissected 1135 parous Culicoides females, the sporozoites of Haemoproteus asymmetricus (genetic lineage hTUPHI01) have been detected for the first time in the salivary glands of Culicoides festivipennis. The sporozoites of four Haemoproteus lineages were detected in Culicoides segnis, C. festivipennis, and Culicoides kibunensis biting midges. PCR-based screening showed that the females of seven Culicoides species were naturally infected with Haemoproteus parasites. The DNA of the parasite of owls, Haemoproteus syrnii (hSTAL2), was detected for the first time in Culicoides punctatus. The highest abundance of collected Culicoides females was in June, but the highest prevalence of Haemoproteus parasites in biting midges was in July. The abundance of Culicoides was higher in the woodland compared with reeds during the season. The acquired findings indicate the varied abundance and diversity of biting midges throughout the season and across distinct habitats. This variability could potentially impact the transmission of Haemoproteus parasites among birds with diverse breeding site ecologies. These outcomes hold the potential to enhance our understanding of the epizootiology of Haemoproteus infections within temperate climatic zones.

A survey on management practices and attitudes of broiler buy-back farmers towards farm animal welfare in Gampaha district, Sri Lanka: a case study of a commercial broiler chicken processing company

Contract grower/buy-back farming system is well established in the present poultry industry in Sri Lanka. This study assessed farmer profile, key management practices and attitudes of the buy-back farmers towards broiler chicken welfare. A total of 40 buy-back farmers in Gampaha District, Sri Lanka were interviewed via telephone conversations using an open structured type questionnaire. Data were statistically analyzed using SPSS version 23.0. Relationships among variables were computed by Ordinal Logistic Regression. Majority (56%) of the farmers were in between the age group of 35-50 y, and 17.6% were females. The most popular flock sizes were in between 1000-5000 birds (64.1%). All the farmers stated that they purposely check for sick or injured birds and 97.4% of them practiced isolation of sick birds. However, no one euthanized severely injured or sick birds. All farmers informed that they practice up-right position when catching and handling birds. Half of the farmers (56.4%) were not well aware of concepts of farm animal welfare. Farmers’ attitudes on farm animal welfare, transportation, and slaughtering were compared with farmers’ profile and resulted in no significant relationship. There was a positive relationship that tend to be significant (P = 0.051) with welfare awareness (YES) vs the welfare positive attitudes on handling of birds. When flock size increased, farmers’ awareness of pain of birds was significantly decreased (P<0.05). In conclusion, a considerable number of buy-back farmers had poor or uncertain attitudes regarding broiler chicken welfare, and their management practices were mostly production-focused. It is suggested that poultry welfare awareness programs would be beneficial to improve farmers' positive attitudes to ensure the welfare of broiler chickens.

Evaluation of factors associated with biosecurity, antimicrobial use and mortality in broiler farms in Northern Kerala

A survey was conducted (March 2020 to October 2020) on biosecurity practices, disease occurrence and antimicrobial usage of 77 broiler farms from five districts of Northern Kerala. Data were collected through a questionnaire and field-level disease diagnostic tests were conducted. Biosecurity status varied from farm to farm with 97.4 per cent promoted vaccination and 61.04 per cent disposed carcasses by burning. However, limitations were observed in the use of a footbath, quarantine of new stock, isolation of diseased birds and quality of water. The five most common diseases recorded were Chronic respiratory disease (48.1%), Acute Death Syndrome (27.3%), Colibacillosis (23.4%), Pullorum (18.2%) and Coccidiosis (18.2%). The commonly used antibiotics in poultry farms were Enrofloxacin (35.1%), Cephalexin (14.3%), Tylosin (11.7%) and Levofloxacin (10.4%). Some of the farmers (14.3%) were unaware of the antibiotics used in their farms, a potent risk factor for the emergence of antimicrobial resistance. About 19.49 per cent of farms restricted antibiotic use and 44.15 per cent of farms supported herbal traditional medicines as an alternative to antimicrobials.

Host-associated variability of the cdtABC operon, coding for the cytolethal distending toxin, in Campylobacter jejuni.

Campylobacter, a major cause of food-borne gastroenteritis worldwide, colonize the gastrointestinal tract of a wide range of animals, being birds the main reservoir. The mechanisms involved in the interaction of Campylobacter with the different hosts are poorly understood. The cytolethal distending toxin, encoded in the cdtABC operon, is considered a pivotal virulence factor during human infection. Differences in the prevalence of cdtABC genes in Campylobacter isolates from three distinct origins (wild birds, broiler chickens and humans) prompted us to further characterize their allelic variability. The sequence of cdtABC is highly conserved among broiler and human isolates. A high diversity of cdtABC alleles was found among wild bird isolates, including several alleles that do not produce any functional CDT. These results suggest that specific variants of the cdtABC operon might define the host range of specific Campylobacter jejuni isolates. Moreover, our data indicate that PCR methodology is inaccurate to characterize the prevalence of the cdt genes, since negative PCR detection can be the result of divergences in the sequence used for primer design rather than indicating the absence of a specific gene.

Intra-species diversity of Clostridium perfringens: A diverse genetic repertoire reveals its pathogenic potential

Clostridium perfringens is the causative agent of many enterotoxic diseases in humans and animals, and it is present in diverse environments (soil, food, sewage, and water). Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) have provided a general approach about genetic diversity of C. perfringens; however, those studies are limited to specific locations and often include a reduced number of genomes. In this study, 372 C. perfringens genomes from multiple locations and sources were used to assess the genetic diversity and phylogenetic relatedness of this pathogen. In silico MLST was used for typing the isolates, and the resulting sequence types (ST) were assigned to clonal complexes (CC) based on allelic profiles that differ from its founder by up to double-locus variants. A pangenome analysis was conducted, and a core genome-based phylogenetic tree was created to define phylogenetic groups. Additionally, key virulence factors, toxinotypes, and antibiotic resistance genes were identified using ABRicate against Virulence Factor Database (VFDB), TOXiper, and Resfinder, respectively. The majority of the C. perfringens genomes found in publicly available databases were derived from food (n = 85) and bird (n = 85) isolates. A total of 195 STs, some of them shared between sources such as food and human, horses and dogs, and environment and birds, were grouped in 25 CC and distributed along five phylogenetic groups. Fifty-three percent of the genomes were allocated to toxinotype A, followed by F (32%) and G (7%). The most frequently found virulence factors based on > 70% coverage and 99.95% identity were plc (100%), nanH (99%), ccp (99%), and colA (98%), which encode an alpha-toxin, a sialidase, an alpha-clostripain, and a collagenase, respectively, while tetA (39.5%) and tetB (36.2%), which mediate tetracycline resistance determinants, were the most common antibiotic resistance genes detected. The analyses conducted here showed a better view of the presence of this pathogen across several host species. They also confirm that the genetic diversity of C. perfringens is based on a large number of virulence factors that vary among phylogroups, and antibiotic resistance markers, especially to tetracyclines, aminoglycosides, and macrolides. Those characteristics highlight the importance of C. perfringens as a one of the most common causes of foodborne illness.

Multilocus Sequence Typing and Virulence Potential of Vibrio parahaemolyticus Strains Isolated from Aquatic Bird Feces.

ABSTRACTVibrio parahaemolyticus is a Gram-negative, foodborne pathogenic bacterium that causes human gastroenteritis. This organism is ubiquitously present in the marine environment. Detection of V. parahaemolyticus in aquatic birds has been previously reported; however, the characterization of isolates of this bacterium recovered from these birds remains limited. The present study isolated and characterized V. parahaemolyticus from aquatic bird feces at the Bangpu Recreation Center (Samut Prakan province, Thailand) from 2016 to 2017, using multilocus sequence typing (MLST) and genome analysis. The results showed that V. parahaemolyticus was present in 34.9% (76/218) of the collected bird fecal samples. Among the ldh-positive V. parahaemolyticus isolates (n = 308), 1% (3/308) were positive for tdh, 1.3% (4/308) were positive for trh, and 0.3% (1/308) were positive for both tdh and trh. In turn, the MLST analysis revealed that 49 selected V. parahaemolyticus isolates resolved to 36 STs, 26 of which were novel (72.2%). Moreover, a total of 10 identified STs were identical to globally reported pathogenic strains (ST1309, ST1919, ST491, ST799, and ST2516) and environmental strains (ST1879, ST985, ST288, ST1925, and ST260). The genome analysis of isolates possessing tdh and/or trh (ST985, ST1923, ST1924, ST1929 and ST2516) demonstrated that the organization of the T3SS2α and T3SS2β genes in bird fecal isolates were almost identical to those of human clinical strains posing public health concerns of pathogen dissemination in the recreational area. The results of this study suggest that aquatic birds are natural reservoirs of new strains with high genetic diversity and are alternative sources of potentially pathogenic V. parahaemolyticus in the marine environment.IMPORTANCE To our knowledge, infection of foodborne bacterium V. parahamolyticus occurs via the consumption of undercooked seafood contaminated with pathogenic strains. Aquatic bird is a neglectable source that can transmit V. parahaemolyticus along coastal areas. This study reported the detection of potentially pathogenic V. parahamolyticus harboring virulence genes from aquatic bird feces at the recreational center situated near the Gulf of Thailand. These strains shared identical genetic profile to the clinical isolates that previously reported in many countries. Furthermore, the strains from aquatic birds showed extremely high genetic diversity. Our research pointed out that the aquatic bird is possibly involved in the evolution of novel strains of V. parahaemolyticus and play a role in dissimilation of the potentially pathogenic strains across geographical distance.

Description of the two novel species of the genus Helicobacter: Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., isolated from feces of urban wild birds

A total of 26 Gram-negative, motile, gently curved, and rod-shaped isolates were recovered, during a study to determine the faeco-prevalence of Helicobacter spp. in urban wild birds. Pairwise comparisons of the 16S rRNA gene sequences indicated that these isolates belonged to the genus Helicobacter and phylogenetic analysis based on the 16S rRNA gene sequences showed that the isolates were separated into two divergent groups. The first group consisted of 20 urease-positive isolates sharing the highest 16S rRNA gene sequence identity levels of 98.5–98.6% to H. mustelae ATCC 43772T, while the second group contained six urease-negative isolates with the sequence identity level of 98.5% to the type strain of H. pametensis ATCC 51478T. Five isolates were chosen and subjected to comparative whole-genome analysis. The phylogenetic analysis of the 16S rRNA, gyrA and atpA gene sequences showed that Helicobacter isolates formed two separate phylogenetic clades, differentiating the isolates from the other Helicobacter species. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains faydin-H8T, faydin-H23T and their close neighbors H. anseris MIT 04-9362T and H. pametensis ATCC 51478T, respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G+C contents of the strains faydin-H8T and faydin-H23T are 32.0% and 37.6%, respectively. The results obtained for the characterization of the wild bird isolates indicate that they represent two novel species, for which the names Helicobacter anatolicus sp. nov., and Helicobacter kayseriensis sp. nov., are proposed, with faydin-H8T(=LMG 32237T = DSM 112312T) and faydin-H23T(=LMG 32236T = CECT 30508T) as respective type strains.

Campylobacter in Wild Birds: Is It an Animal and Public Health Concern?

Campylobacteriosis continues to be one of the leading causes of foodborne bacterial zoonotic infections worldwide. Despite its public health importance, the status of this disease in wild birds and the possibility of transmission from wild birds to domestic animals and humans have not been clearly elucidated yet. This article reviews the available literature with the aim of making a comprehensive manuscript on this disease status in wild birds and the possibility of interspecies transmission. Campylobacter has been isolated from various species of wild birds worldwide, with C. jejuni being the most commonly isolated species. The prevalence of Campylobacter in wild birds may vary depending on several factors like geographical location, season, the bird’s health status, bird species, sample type, the method used, and ecological factors. Molecular studies over the past two to three decades have characterized Campylobacter strains isolated from wild birds and have come up with results that fall into two categories. The first are those that report overlapping strains among human, domestic animal, and wild bird isolates. The results of the studies under this category emphasize that wild birds carry strains of Campylobacter, which are indistinguishable from domestic animals and humans and are therefore an important public and animal health concern. In contrast, the studies under the second category highlight significant differences in Campylobacter population structure among these hosts. Despite the controversiality and the inadequacy of current research to draw a full conclusion, the role of wild birds in the epidemiology of Campylobacter should not be undermined as drug-resistant strains, especially resistance to tetracycline and fluoroquinolones, are increasingly documented. In addition, source attribution studies have linked human cases of Campylobacter infections to wild birds. Therefore, the role of wild birds in the epidemiology of Campylobacter infection should not be neglected. However, in order to determine disease status in wild birds and the precise role of wild birds in domestic animals and human health, detail-oriented epidemiological investigations characterizing the genetic relatedness of isolates from the respective species and environment through one health approach are warranted.

Analisis Kestabilan Model Insidensi Setengah Jenuh pada Epidemi Flu Burung

Abstract: The H5N1 avian influenza is an example of a pathogen that is known to cause human disease outbreaks. This study focuses on selecting avian influenza control strategies using Half-Saturated Incidence (HSI) Models. In this study, a model was constructed by involving elements of human self-protection, poultry isolation and poultry vaccination. Furthermore, it is shown that the parameters that influence are the parameters of the population that apply personal protection and its effectiveness, the parameters of the rate of isolation of birds with avian influenza, and the parameters of vaccine coverage and its effectiveness. Increasing the value of this parameter can reduce the basic reproduction number so that disease-free conditions can occur. Hence, controlling the dynamics of disease spread can be done by increasing the value of these parameters.

Isolation and characterization of Escherichia albertii from wild and safeguarded animals in Okayama Prefecture and its prefectural borders, Japan.

Escherichia albertii has recently been recognized as a zoonotic enteropathogen associated with food poisoning. The reservoirs and transmission routes of this bacterium to humans are still unclear. In this study, we performed a survey of E. albertii in fecal specimens of wild and safeguarded animals in Okayama Prefecture and its prefectural borders, Japan to understand its reservoir in the environment. Forty-two E. albertii were isolated from 10 and 31 droppings of 59 crows and 125 starlings, respectively. Fifty-two E. albertii were isolated from 906 mammal droppings, and out of 52 isolates, origin of 33, 6 and 1 isolates were from martens, foxes, and rabbit, respectively, however, origin of 12 isolates remained unknown. Three E. albertii were isolated from two and one feces of 159 dogs and 76 cats, respectively. Pulsed-filed gel electrophoresis analysis grouped 97 E. albertii strains into 66 pulsotypes including 36 and 30 pulsotypes of isolates from mammals and birds, respectively. E. albertii strains isolated in this study were genetically diverse. Although clonal relationship was not observed between mammal and bird isolates, there were intra- and inter-species relationship in mammalian isolates. All E. albertii strains were positive for eae and Eacdt virulence genes. Furthermore, 20 and 7 strains also carried Eccdt-I and stx2f genes, respectively. Taken together, the results indicate that genetically diverse and potentially virulent E. albertii are distributed among various wild and safeguarded animals in Okayama Prefecture, and the animals could also be reservoirs of E. albertii.

Low occurrence of multi-antimicrobial and heavy metal resistance in Salmonella enterica from wild birds in the United States.

Wild birds are common reservoirs of Salmonella enterica. Wild birds carrying resistant S. enterica may pose a risk to public health as they can spread the resistant bacteria across large spatial scales within a short time. Here, we whole-genome sequenced 375 S. enterica strains from wild birds collected in 41 U.S. states during 1978-2019 to examine bacterial resistance to antibiotics and heavy metals. We found that Typhimurium was the dominant S. enterica serovar, accounting for 68.3% (256/375) of the bird isolates. Furthermore, the proportions of the isolates identified as multi-antimicrobial resistant (multi-AMR: resistant to at least three antimicrobial classes) or multi-heavy metal resistant (multi-HMR: resistant to at least three heavy metals) were both 1.87% (7/375). Interestingly, all the multi-resistant S. enterica (n= 12) were isolated from water birds or raptors; none of them was isolated from songbirds. Plasmid profiling demonstrated that 75% (9/12) of the multi-resistant strains carried resistance plasmids. Our study indicates that wild birds do not serve as important reservoirs of multi-resistant S. enterica strains. Nonetheless, continuous surveillance for bacterial resistance in wild birds is necessary because the multi-resistant isolates identified in this study also showed close genetic relatedness with those from humans and domestic animals.

Epitope Peptide-Based Predication and Other Functional Regions of Antigenic F and HN Proteins of Waterfowl and Poultry Avian Avulavirus Serotype-1 Isolates From Uganda.

Uganda is a Newcastle disease (ND) endemic country where the disease is controlled by vaccination using live LaSota (genotype II) and I2 (genotype I) vaccine strains. Resurgent outbreak episodes call for an urgent need to understand the antigenic diversity of circulating wild Avian Avulavirus serotype-1 (AAvV-1) strains. High mutation rates and the continuous emergence of genetic and antigenic variants that evade immunity make non-segmented RNA viruses difficult to control. Antigenic and functional analysis of the key viral surface proteins is a crucial step in understanding the antigen diversity between vaccine lineages and the endemic wild ND viruses in Uganda and designing ND peptide vaccines. In this study, we used computational analysis, phylogenetic characterization, and structural modeling to detect evolutionary forces affecting the predicted immune-dominant fusion (F) and hemagglutinin-neuraminidase (HN) proteins of AAvV-1 isolates from waterfowl and poultry in Uganda compared with that in LaSota vaccine strain. Our findings indicate that mutational amino acid variations at the F protein in LaSota strain, 25 poultry wild-type and 30 waterfowl wild-type isolates were distributed at regions including the functional domains of B-cell epitopes or N-glycosylation sites, cleavage site, fusion site that account for strain variations. Similarly, conserved regions of HN protein in 25 Ugandan domestic fowl isolates and the representative vaccine strain varied at the flanking regions and potential linear B-cell epitope. The fusion sites, signal peptides, cleavage sites, transmembrane domains, potential B-cell epitopes, and other specific regions of the two protein types in vaccine and wild viruses varied considerably at structure by effective online epitope prediction programs. Cleavage site of the waterfowl isolates had a typical avirulent motif of 111GGRQGR'L117 with the exception of one isolate which showed a virulent motif of 111GGRQKR'F117. All the poultry isolates showed the 111GRRQKR'F117 motif corresponding to virulent strains. Amino acid sequence variations in both HN and F proteins of AAvV-1 isolates from poultry, waterfowl, and vaccine strain were distributed over the length of the proteins with no detectable pattern, but using the experimentally derived 3D structure data revealed key-mapped mutations on the surfaces of the predicted conformational epitopes encompassing the experimental major neutralizing epitopes. The phylogenic tree constructed using the full F gene and partial F gene sequences of the isolates from poultry and waterfowl respectively, showed that Ugandan ND aquatic bird and poultry isolates share some functional amino acids in F sequences yet do remain unique at structure and the B-cell epitopes. Recombination analyses showed that the C-terminus and the rest of the F gene in poultry isolates originated from prevalent velogenic strains. Altogether, these could provide rationale for antigenic diversity in wild ND isolates of Uganda compared with the current ND vaccine strains.

Gut microbiota in two recently diverged passerine species: evaluating the effects of species identity, habitat use and geographic distance

BackgroundIt has been proposed that divergence in the gut microbiota composition between incipient species could contribute to their reproductive isolation. Nevertheless, empirical evidence for the role of gut microbiota in speciation is scarce. Moreover, it is still largely unknown to what extent closely related species in the early stages of speciation differ in their gut microbiota composition, especially in non-mammalian taxa, and which factors drive the divergence. Here we analysed the gut microbiota in two closely related passerine species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia). The ranges of these two species overlap in a secondary contact zone, where both species occasionally hybridize and where interspecific competition has resulted in habitat use differentiation.ResultsWe analysed the gut microbiota from the proximal, middle and distal part of the small intestine in both sympatric and allopatric populations of the two nightingale species using sequencing of bacterial 16S rRNA. We found small but significant differences in the microbiota composition among the three gut sections. However, the gut microbiota composition in the two nightingale species did not differ significantly between either sympatric or allopatric populations. Most of the observed variation in the gut microbiota composition was explained by inter-individual differences.ConclusionsTo our knowledge, this is the first attempt to assess the potential role of the gut microbiota in bird speciation. Our results suggest that neither habitat use, nor geographical distance, nor species identity have strong influence on the nightingale gut microbiota composition. This suggests that changes in the gut microbiota composition are unlikely to contribute to reproductive isolation in these passerine birds.