Epidemiological evidence that garden birds are a source of human salmonellosis in England and Wales

Continuous surveillance of pathogens detects excretion of avian orthoreovirus and parvovirus by several wild waterfowl: possible wild bird reservoirs

Migratory wild birds can carry various pathogens, such as influenza A virus, which can spread to globally and cause disease outbreaks and epidemics. Continuous epidemiological surveillance of migratory wild birds is of great significance for the early warning, prevention, and control of epidemics. To investigate the pathogen infection status of migratory wild birds in eastern China, fecal samples were collected from wetlands to conduct pathogen surveillance. The results showed that duck orthoreovirus (DRV) and goose parvovirus (GPV) nucleic acid were detected positive in the fecal samples collected from wild ducks, egrets, and swan. Phylogenetic analysis of the amplified viral genes reveals that the isolates were closely related to the prevalent strains in the regions involved in East Asian-Australasian (EAA) migratory flyway. Phylogenetic analysis of the amplified viral genes confirmed that they were closely related to circulating strains in the regions involved in the EAA migration pathway. The findings of this study have expanded the host range of the orthoreovirus and parvovirus, and revealed possible virus transmission between wild migratory birds and poultry.

The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States

The serovars of Salmonella enterica display dramatic differences in pathogenesis and host preferences. We developed a process (patent pending) for grouping Salmonella isolates and serovars by their public health risk. We collated a curated set of 12,337 S. enterica isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits We then grouped isolates (virulence clusters) using hierarchical clustering (Ward's method), used non-parametric bootstrapping to assess cluster stability, and externally validated the clusters against epidemiological virulence measures from FoodNet, the National Outbreak Reporting System (NORS), and US federal sampling of beef products. We identified five stable virulence clusters of S. enterica serovars. Cluster 1 (higher virulence) serovars yielded an annual incidence rate of domestically acquired sporadic cases roughly one and a half times higher than the other four clusters combined (Clusters 2-5, lower virulence). Compared to other clusters, cluster 1 also had a higher proportion of infections leading to hospitalization and was implicated in more foodborne and beef-associated outbreaks, despite being isolated at a similar frequency from beef products as other clusters. We also identified subpopulations within 11 serovars. Remarkably, we found S. Infantis and S. Typhimurium subpopulations that significantly differed in genome length and clinical case presentation. Further, we found that the presence of the pESI plasmid accounted for the genome length differences between the S. Infantis subpopulations. Our results show that S. enterica strains associated with highest incidence of human infections share a common virulence repertoire. This work could be updated regularly and used in combination with foodborne surveillance information to prioritize serovars of public health concern.

Human Salmonellosis Outbreak Linked to Salmonella Typhimurium Epidemic in Wild Songbirds, United States, 2020-2021

Salmonella infection causes epidemic death in wild songbirds, with potential to spread to humans. In February 2021, public health officials in Oregon and Washington, USA, isolated a strain of Salmonella enterica serovar Typhimurium from humans and a wild songbird. Investigation by public health partners ultimately identified 30 illnesses in 12 states linked to an epidemic of Salmonella Typhimurium in songbirds. We report a multistate outbreak of human salmonellosis associated with songbirds, resulting from direct handling of sick and dead birds or indirect contact with contaminated birdfeeders. Companion animals might have contributed to the spread of Salmonella between songbirds and patients; the outbreak strain was detected in 1 ill dog, and a cat became ill after contact with a wild bird. This outbreak highlights a One Health issue where actions like regular cleaning of birdfeeders might reduce the health risk to wildlife, companion animals, and humans.

Backyard zoonoses: The roles of companion animals and peri-domestic wildlife

The spillover of human infectious diseases from animal reservoirs is now well appreciated. However, societal and climate-related changes are affecting the dynamics of such interfaces. In addition to the disruption of traditional wildlife habitats, in part because of climate change and human demographics and behavior, there is an increasing zoonotic disease risk from companion animals. This includes such factors as the awareness of animals kept as domestic pets and increasing populations of free-ranging animals in peri-domestic environments. This review presents background and commentary focusing on companion and peri-domestic animals as disease risk for humans, taking into account the human-animal interface and population dynamics between the animals themselves.

Whole-Genome Subtyping Reveals Population Structure and Host Adaptation of Salmonella Typhimurium from Wild Birds

Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. However, the work remained largely underexplored at a strain level until the advent of whole-genome sequencing (WGS). Here, we performed WGS-based subtyping and analyses of Salmonella enterica serovar Typhimurium (n = 787) from different wild birds across 18 countries over a 75-year period. We revealed seven avian host-associated S. Typhimurium variants/lineages. These lineages emerged globally over short timescales and presented genetic features distinct from S. Typhimurium lineages circulating among humans and domestic animals. We further showed that, in terms of virulence, host adaptation of these variants was driven by genome degradation. Our results provide a snapshot of the population structure and genetic diversity of S. Typhimurium within avian hosts. We also demonstrate the value of WGS-based subtyping and analyses in unravelling closely related variants at the strain level.

Genome-based risk assessment for foodborne Salmonella enterica from food animals in China: A One Health perspective

Salmonella is one of the most common causes of foodborne bacterial disease. Animal-borne foods are considered the primary sources of Salmonella transmission to humans. However, genomic assessment of antimicrobial resistance (AMR) and virulence of Salmonella based on One Health approach remains obscure in China. For this reason, we analyzed the whole genome sequencing data of 134 Salmonella isolates recovered from different animal and meat samples in China. The 134 Salmonella were isolated from 2819 samples (4.75 %) representing various sources (pig, chicken, duck, goose, and meat) from five Chinese provinces (Zhejiang, Guangdong, Jiangxi, Hunan, and Qinghai). AMR was evaluated by the broth dilution method using 13 different antimicrobial agents, and results showed that 85.82 % (115/134) of isolates were resistant to three or more antimicrobial classes and were considered multidrug-resistant (MDR). Twelve sequence types (STs) were detected, with a dominance of ST469 (29.85 %, 40/134). The prediction of virulence genes showed the detection of cdtB gene encoding typhoid toxins in one isolate of S. Muenster recovered from chicken, while virulence genes associated with type III secretion systems were detected in all isolates. Furthermore, plasmid-type prediction showed the abundance of IncFII(S) (13/134; 9.7 %) and IncFIB(S) (12/134; 8.95 %) in the studied isolates. Together, this study demonstrated the ability to use whole-genome sequencing (WGS) as a cost-effective method to provide comprehensive knowledge about foodborne Salmonella isolates in One Health surveillance approach.

The genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain

Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which is typically misidentified as pathotypes of diarrhoeagenic Escherichia coli or Shigella species and is generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated, and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans (n = 83) and birds (n = 79) isolated in Great Britain between 2000 and 2021 and analysed these alongside a broader public dataset (n = 475) to address these gaps. We found human and avian isolates typically (90%; 148/164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance profiles. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98-35.45 p = 0.0002) in finches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii.

Escherichia coli Isolated from Vegans, Vegetarians and Omnivores: Antibiotic Resistance, Virulence Factors, Pathogenicity Islands and Phylogenetic Classification

Pathogenic strains of Escherichia coli have acquired virulence factors, which confer an increased ability to cause a broad spectrum of enteric diseases and extraintestinal infections. The aim of this study was to analyze the antimicrobial resistance profile of and the presence of virulence-associated genes (VAGs) in E. coli fecal isolates from omnivores, vegetarians and vegans. A control group of 60 isolates from omnivores, as well as a study group with 41 isolates from vegetarians and 17 from vegans, were analyzed. Isolates from both groups showed a high rate of resistance to ampicillin, amoxicillin-clavulanic acid and nalidixic acid, and some of them were positive for the ESBL test (12% of isolates from vegetarians/vegans and 5% of isolates from omnivores). The most predominant VAGs detected in isolates from omnivores were fimH (70%), iutA (32%), fyuA (32%) and traT (32%), while among isolates from vegetarians or vegans, the most predominant were traT (62%), kpsMT k1 (28%) and iutA (22%). Most isolates from omnivores (55%) were positive for PAI I536, while most of those from vegetarians/vegans (59%) were positive for PAI IV536. Phylogenetic group A, composed of commensal non-pathogenic isolates that survive in the intestinal tract, was the most prevalent in both control and study groups. Some VAGs were found in only one of the groups, such as the pathogenicity island PAI III536, found in 12% of the isolates from omnivores, while the kpsMT III gene (15%) was detected only among isolates from vegetarians/vegans. Interestingly, this gene codes for a polysaccharide capsule found mainly in E. coli isolates causing intestinal infections, including EPEC, ETEC and EHEC. Finally, our results show that there were no advantages in vegetarian or vegan diets compared to the omnivorous diet, as in both groups we detected isolates harboring VAGs and displaying resistance to antibiotics, especially those most commonly used to treat urinary tract infections.

Comparative Genomic Analysis of Salmonella enterica Serovar Typhimurium Isolates from Passerines Reveals Two Lineages Circulating in Europe, New Zealand, and the United States

Salmonella enterica serovar Typhimurium strains from passerines have caused wild bird deaths and human salmonellosis outbreaks in Europe, Oceania, and North America. Here, we performed comparative genomic analysis to explore the emergence, genetic relationship, and evolution of geographically dispersed passerine isolates. We found that passerine isolates from Europe and the United States clustered to form two lineages (EU and US passerine lineages), which were distinct from major S. Typhimurium lineages circulating in other diverse hosts (e.g., humans, cattle, pigs, chickens, and other avian hosts, such as pigeons and ducks). Further, passerine isolates from New Zealand clustered to form a sublineage (NZ passerine lineage) of the US passerine lineage. We inferred that the passerine isolates mutated at a rate of 3.2 × 10-7 substitutions/site/year, and the US, EU, and NZ passerine lineages emerged in approximately 1952, 1970, and 1996, respectively. Isolates from the three lineages presented genetic similarity, such as lack of antimicrobial resistance genes and accumulation of the same virulence pseudogenes. In addition, genetic diversity due to microevolution existed in the three passerine lineages. Specifically, pseudogenization in the type 1 fimbrial gene fimC (deletion of G at position 87) was detected only in the US and NZ passerine isolates, while single-base deletions in type 3 secretion system effector genes (i.e., gogB, sseJ, and sseK2) cooccurred solely in the EU passerine isolates. These findings provide insights into the evolution, host adaptation, and epidemiology of S. Typhimurium in passerines. IMPORTANCE Passerine-associated S. Typhimurium strains have been linked to human salmonellosis outbreaks in recent years. Here, we investigated the phylogenetic relationship of globally distributed passerine isolates and profiled their genomic similarity and diversity. Our study reveals two passerine-associated S. Typhimurium lineages circulating in Europe, Oceania, and North America. Isolates from the two lineages presented phylogenetic and genetic signatures that were distinct from those of isolates from other hosts. The findings shed light on the host adaptation of S. Typhimurium in passerines and are important for source attribution of S. Typhimurium strains to avian hosts. Further, we found that S. Typhimurium definitive phage type 160 (DT160) from passerines, which caused decades-long human salmonellosis outbreaks in New Zealand and Australia, formed a sublineage of the US passerine lineage, suggesting that DT160 might have originated from passerines outside Oceania. Our study demonstrates the importance of whole-genome sequencing and genomic analysis of historical microbial collections to modern epidemiologic surveillance.

Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA

The evolution of Salmonella enterica serovar Typhimurium (S. Typhimurium) within passerines has resulted in pathoadaptation of this serovar to the avian host in Europe. Recently, we identified an S. Typhimurium lineage from passerines in North America. The emergence of passerine-adapted S. Typhimurium in Europe and North America raises questions regarding its evolutionary origin. Here, we demonstrated that the UK and US passerine-adapted S. Typhimurium shared a common ancestor from ca. 1838, and larids played a key role in the clonal expansion by disseminating the common ancestor between North America and Europe. Further, we identified virulence gene signatures common in the passerine- and larid-adapted S. Typhimurium, including conserved pseudogenes in fimbrial gene lpfD and Type 3 Secretion System (T3SS) effector gene steC. However, the UK and US passerine-adapted S. Typhimurium also possessed unique virulence gene signatures (i.e. pseudogenes in fimbrial gene fimC and T3SS effector genes sspH2, gogB, sseJ and sseK2), and the majority of them (38/47) lost a virulence plasmid pSLT that was present in the larid-adapted S. Typhimurium. These results provide evidence that passerine-adapted S. Typhimurium share a common ancestor with those from larids, and the divergence of passerine- and larid-adapted S. Typhimurium might be due to pseudogenization or loss of specific virulence genes.

Salmonella enterica serovar Typhimurium from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type

Salmonella enterica serovar Typhimurium is typically considered a host generalist; however, certain isolates are associated with specific hosts and show genetic features of host adaptation. Here, we sequenced 131 S. Typhimurium isolates from wild birds collected in 30 U.S. states during 1978–2019. We found that isolates from broad taxonomic host groups including passerine birds, water birds (Aequornithes), and larids (gulls and terns) represented three distinct lineages and certain S. Typhimurium CRISPR types presented in individual lineages. We also showed that lineages formed by wild bird isolates differed from most isolates originating from domestic animal sources, and that genomes from these lineages substantially improved source attribution of Typhimurium genomes to wild birds by a machine learning classifier. Furthermore, virulence gene signatures that differentiated S. Typhimurium from passerines, water birds, and larids were detected. Passerine isolates tended to lack S. Typhimurium-specific virulence plasmids. Isolates from the passerine, water bird, and larid lineages had close genetic relatedness with human clinical isolates, including those from a 2021 U.S. outbreak linked to passerine birds. These observations indicate that S. Typhimurium from wild birds in the United States are likely host-adapted, and the representative genomic data set examined in this study can improve source prediction and facilitate outbreak investigation.

IMPORTANCE Within-host evolution of S. Typhimurium may lead to pathovars adapted to specific hosts. Here, we report the emergence of disparate avian S. Typhimurium lineages with distinct virulence gene signatures. The findings highlight the importance of wild birds as a reservoir for S. Typhimurium and contribute to our understanding of the genetic diversity of S. Typhimurium from wild birds. Our study indicates that S. Typhimurium may have undergone adaptive evolution within wild birds in the United States. The representative S. Typhimurium genomes from wild birds, together with the virulence gene signatures identified in these bird isolates, are valuable for S. Typhimurium source attribution and epidemiological surveillance.

New analytical methods using carbon-based nanomaterials for detection of Salmonella species as a major food poisoning organism in water and soil resources

Salmonella is one of the most prevalent causing agents of food- and water-borne illnesses, posing an ongoing public health threat. These food-poisoning bacteria contaminate the resources at different stages such as production, aggregation, processing, distribution, as well as marketing. According to the high incidence of salmonellosis, effective strategies for early-stage detection are required at the highest priority. Since traditional culture-dependent methods and polymerase chain reaction are labor-intensive and time-taking, identification of early and accurate detection of Salmonella in food and water samples can prevent significant health economic burden and lessen the costs. The immense potentiality of biosensors in diagnosis, such as simplicity in operation, the ability of multiplex analysis, high sensitivity, and specificity, have driven research in the evolution of nanotechnology, innovating newer biosensors. Carbon nanomaterials enhance the detection sensitivity of biosensors while obtaining low levels of detection limits due to their possibility to immobilize huge amounts of bioreceptor units at insignificant volume. Moreover, conjugation and functionalization of carbon nanomaterials with metallic nanoparticles or organic molecules enables surface functional groups. According to these remarkable properties, carbon nanomaterials are widely exploited in the development of novel biosensors. To be specific, carbon nanomaterials such as carbon nanotubes, graphene and fullerenes function as transducers in the analyte recognition process or surface immobilizers for biomolecules. Herein the potential application of carbon nanomaterials in the development of novel Salmonella biosensors platforms is reviewed comprehensively. In addition, the current problems and critical analyses of the future perspectives of Salmonella biosensors are discussed.

Low occurrence of Salmonella spp. in wild birds from a Swiss rehabilitation centre

BACKGROUND

Salmonella are bacteria of the family Enterobacteriaceae with a wide host range. Infection in birds causes subclinical disease to mass mortality events. Wild birds may act as healthy carriers posing a hazard to livestock and humans. The present study investigated the occurrence of Salmonella in wild birds admitted to a rehabilitation centre in order to assess the exposure of the staff to this zoonotic pathogen.

METHODS

Faecal swabs of 552 avian patients (68 species) were collected over the course of 12 months. Each sample was propagated in enrichment broth and subsequently incubated on a RAPID'Salmonella plate. Salmonella isolates were serotyped, and antimicrobial susceptibility testing was performed.

RESULTS

Six Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and 1 S. Schleissheim were detected; all were pansusceptible to the antibiotics tested.

CONCLUSION

Despite the low positive rate in the tested population, the authors recommend applying protective equipment and hygiene measures when handling wild birds.

What WGS Reveals about Salmonella enterica subsp. enterica in Wildlife in Germany

The aim of this study was to gain an overview of the genetic diversity of Salmonella found in wildlife in Germany. We were particularly interested in exploring whether wildlife acts as a reservoir of certain serovars/subtypes or antimicrobial resistance (AMR) genes. Moreover, we wanted to explore the potential of Salmonella in spreading from wildlife to livestock and humans. To answer these questions, we sequenced 260 Salmonella enterica subsp. enterica isolates sampled between 2002 and 2020 from wildlife across Germany, using short-read whole genome sequencing. We found, consistent with previous findings, that some Salmonella sequence types are associated with certain animal species, such as S. Choleraesuis ST145 with wild boar and S. Enteritidis ST183 with hedgehogs. Antibiotic resistance was detected in 14.2% of all isolates, with resistance against important WATCH group antibiotics present in a small number of isolates. We further found that wildlife isolates do not form separate phylogenetic clusters distant to isolates from domestic animals and foodstuff, thus indicating frequent transmission events between these reservoirs. Overall, our study shows that Salmonella in German wildlife are diverse, with a low AMR burden and close links to Salmonella populations of farm and food-production environments.

Animal source food eating habits of outpatients with antimicrobial resistance in Bukavu, D.R. Congo

BACKGROUND

Antibiotic resistance is a public health concern in Democratic Republic Congo and worldwide. It is usually caused by antibiotic over prescription or dispensing practices. The consumption of animal source food (ASF) could be another source of antibiotic resistance but is rarely studied. The objective of the study was to evaluate the eating habits of ASF by outpatients with antimicrobial resistance through an analysis of (i) the association of their antimicrobial resistance with ASF consumption; (ii) the influence of the types of ASF on their antimicrobial resistance.

METHODS

This is a retrospective analytical study conducted at three major Hospitals in Bukavu City (D. R. Congo). A total number of 210 patients, whose samples (mainly faeces and urine) had been subjected to bacterial examination, was included in this study. Morphological, biochemical and antibiotic susceptibility (using disc diffusion method) tests were performed on the samples. This served to isolate and identify resistant bacteria. Afterwards, patients responded to questions about the types and quantity of ASF eaten in the last week. We analysed data using descriptive statistics, logistic regression and non-parametric ranking tests.

RESULTS

Escherichia coli (37.1%), Klebsiella pneumonae (14.7%), and Staphylococcus aureus (13.8%) were the most prevalent bacteria. E. coli (68.4%) and K. pneumonae (87.5%) were multidrug resistant (MDR), while S. aureus (7.7%) was minor. Low beef (O.R. 0.737, C.I. 0.542-1.002) and pork (O.R. 0.743, C.I. 0.560 - 0.985) consumption led to significantly (p < 0.05) lower risks of resistance to ciprofloxacin. Patients eating three different ASF per week had the highest resistance score (20.67) and high consumption rates of goat meat, pork and milk (41.5%).

CONCLUSION

The findings of this study suggest a contribution of human nutrition to antimicrobial resistance frequency. Our results show the existence of a high prevalence of multi-drug resistant bacteria in patients for which eating beef, pork and drinking milk are major risk factors. Therefore, a stricter control of antibiotic usage in livestock production and of their presence in ASF is recommended.

Lack of Evidence That Bird Feeders Are a Source of Salmonellosis during Winter in Poland

Bird feeders are known to be a transfer site for many important bird pathogens, such as zoonotic Salmonella spp., known to be widespread among wild birds in Poland. The aim of the study was to investigate (1) whether feeders can be a source of Salmonella spp., (2) whether the risk is the same for feeders located in cities and rural areas and (3) whether there is a different level of contamination with Salmonella spp. between old and new feeders. Data were collected in the period 12 January-28 February 2018 in four cities in Poland and nearby rural areas. In total, 204 feeders were sampled. The samples from feeders were taken after a 2-week period of feeding birds. Material for analysis consisted of the remains of food and feces. We did not find the presence of Salmonella spp. in any of the tested samples collected from bird feeders. Therefore, the estimated value of the 95% confidence interval for the binary data was 0.000-0.018. Reasons for the isolation of Salmonella spp. from feeders not being successful lie in the low intensity of bacterial shedding by infected wild birds and low survival of bacteria in the environment in bird feces-which are still not well studied.

Pathoadaptation of the passerine-associated Salmonella enterica serovar Typhimurium lineage to the avian host

Salmonella enterica is a diverse bacterial pathogen and a primary cause of human and animal infections. While many S. enterica serovars present a broad host-specificity, several specialized pathotypes have been adapted to colonize and cause disease in one or limited numbers of host species. The underlying mechanisms defining Salmonella host-specificity are far from understood. Here, we present genetic analysis, phenotypic characterization and virulence profiling of a monophasic S. enterica serovar Typhimurium strain that was isolated from several wild sparrows in Israel. Whole genome sequencing and complete assembly of its genome demonstrate a unique genetic signature that includes the integration of the BTP1 prophage, loss of the virulence plasmid, pSLT and pseudogene accumulation in multiple T3SS-2 effectors (sseJ, steC, gogB, sseK2, and sseK3), catalase (katE), tetrathionate respiration (ttrB) and several adhesion/ colonization factors (lpfD, fimH, bigA, ratB, siiC and siiE) encoded genes. Correspondingly, this strain demonstrates impaired biofilm formation, intolerance to oxidative stress and compromised intracellular replication within non-phagocytic host cells. Moreover, while this strain showed attenuated pathogenicity in the mouse, it was highly virulent and caused an inflammatory disease in an avian host. Overall, our findings demonstrate a unique phenotypic profile and genetic makeup of an overlooked S. Typhimurium sparrow-associated lineage and present distinct genetic signatures that are likely to contribute to its pathoadaptation to passerine birds.

During Salmonella enterica evolution, many different ecological niches have been effectively occupied by this highly diverse bacterial pathogen. While many S. enterica serovars successfully maintained their ability to infect and colonize in a wide-array of host species, a few biotypes have evolved to colonize and cause a disease in only one or a small group of hosts. The evolutionary dynamic and the mechanisms shaping the host-specificity of Salmonella adapted strains are important to better understand Salmonella pathogenicity and its ecology, but still not fully understood. Here, we report genetic and phenotypic characterization of a S. Typhimurium strain that was isolated from several wild sparrows in Israel. This strain presented unique phenotypic profile that included impaired biofilm formation, high sensitivity to oxidative stress and reduced intracellular replication in non-phagocytic cells. In addition, while this strain was able to cause high inflammatory disease in an avian host, it was highly attenuated in the mouse model. Genome analysis identified that specific genetic signatures found in the sparrow strain are more frequently associated with poultry isolates than clinical isolates of S. Typhimurium. These genetic features are expected to accumulatively contribute toward the adaptation of this strain to birds.

Molecular Screening of Salmonella sp. from fecal sample of Sparrows (Passer domesticus) in Yogyakarta, Indonesia

Wild birds is one of the reservoir agent of some of various zoonotic diseases. The study was aim to see the potential of sparrow as the reservoir agent of Salmonella sp. using polymerase chain reaction (PCR) method. We detected the invA gene of Salmonella sp. from faecal sample of sparrows (Passer domesticus) in local area of Yogyakarta, Indonesia. A total of 30 faecal dropping samples were collected from sparrows. DNA was extracted from the faecal samples, then amplified by PCR for the target genes. The amplicons were electrophorized to see the visualization of DNA on the agarose gel. The result showed the prevalence of the positive result of Salmonella sp. was 3,3%. The study indicated that sparrows can spread zoonotic pathogens and this necessitates monitoring for the epidemiologic status of these pathogens among birds, also applying the appropriate intervention measures to prevent the transmission of zoonotic diseasesfrom birds to humans.

Assessing the Food Safety Risk Posed by Birds Entering Leafy Greens Fields in the US Southwest

In the US Southwest, it is common to observe birds in leafy green fields, though the risk they contribute to foodborne outbreaks remains unclear. In this study, we investigated and recorded the relationship between birds near leafy green fields and the risk for contaminated irrigation water or leafy green plants. We monitored the presence of birds for over two years and performed cloacal swab analysis for non-pathogenic Escherichia coli, E. coli O157:H7 and Salmonellaenterica, while also monitoring the incidence of other microbial indicators. We also assessed the risks from bird feces by performing observations in a commercial field reported with Salmonella positive samples and by analyzing the survival of foodborne pathogens in bird feces. Our results showed that most of the birds near the crop fields were resident small birds. We did not observe a correlation between the number of birds in sites and the incidence of indicator bacteria (e.g., coliforms, E. coli) in irrigation canal water, with the exception of one out of four sites where water flow was low or stagnant. Using walk-in-traps, 305 birds were captured and placed in short-term captivity to determine the presence of various bacteria. None of the birds tested positive for E. coli O157:H7 or Salmonella. However, nearly 40% of the birds captured were confirmed positive for non-pathogenic E. coli. We found no correlation between age (young, adult, unknown), gender (male, female, unknown) and the incidence of E. coli positive birds, but we observed significantly higher probability of incidence during October-December. The role of relative humidity and temperature on bacterial survival appeared to play a key role in the survival of Salmonella on the leaves of spinach plants in a commercial field. This was also confirmed in laboratory conditions where Salmonella inoculated in bird feces and exposed to 15 °C and 80% RH(Relative humidity) survived beyond 133 days, while at 26 °C and 40% RH, the organism was undetectable after 63 days. Our results suggest that local birds associated with leafy green fields likely pose a minimal impact of risk for food contamination, but also points out the need for increased analysis specifically for E. coli O157:H7. Furthermore, our study suggests the need for expanding research that addresses risks associated with large migratory birds, especially in areas where stagnated water sources would be used for overhead sprinkle irrigation.

Can domestic pigeon be a potential carrier of zoonotic Salmonella?

Salmonellosis is one of the most important bacterial diseases in pigeons. This study aimed to estimate the prevalence of Salmonella spp. in domestic pigeons (Columba livia f. domestica) in Poland, its antimicrobial susceptibility (both phenotypic and genotypic), and its capability for biofilm formation. The presence of selected virulence genes, nucleotide homology of selected genes, and susceptibility to bacteriophages were investigated as well. From the 585 pigeons tested, 5.47% turned out positive. All isolated strains were recognized as Salmonella enterica ser. Typhimurium. The asymptomatic pigeons were carriers of 37.5% of the isolates. The dominant variants were as follows: 1,4,[5],12,:i:1,2 (53.13%) and 1,4,[5],12,:‐:‐ (31.25%). Most of the strains analysed showed the ability to produce biofilm after 24 and 48 hr of incubation (59.38% and 53.13%, respectively). Over 90% of the strains were confirmed for lpfA, agafA, invA, sivH, and avrA virulence genes. Also, of the thirteen antimicrobial susceptibility genes, the following were confirmed: sul1, tet(A), bla_TEM‐1, floR, strA, and strB. The most common were the strB (18%) and tet(A) (12%) genes that are responsible for coding resistance to aminoglycosides and tetracyclines, respectively. Most of the strains were phenotypically resistant to oxytetracycline (46.88%), neomycin (53.13%) and tylosin (100%). The susceptibility of the investigated Salmonella strains to the bacteriophages was between 33% and 100%. MLST, PCR MP and ERIC PCR analyses indicated a very high genetic similarity of the investigated strains (over 99%). Results of our study indicate that Salmonella enterica ser. Typhimurium is still an important agent in domestic pigeons and that its antimicrobial resistance increases. Alarming is also the confirmation of a single‐phase variant 1,4,[5],12:i,‐, which could have increased virulence and multi‐drug resistance encoded on the plasmid. Most importantly, however, such strains have been isolated from humans with clinical symptoms of Salmonella infection.

Wild birds as reservoirs for diverse and abundant gamma- and deltacoronaviruses

Wild birds interconnect all parts of the globe through annual cycles of migration with little respect for country or continental borders. Although wild birds are reservoir hosts for a high diversity of gamma- and deltacoronaviruses, we have little understanding of the ecology or evolution of any of these viruses. In this review, we use genome sequence and ecological data to disentangle the evolution of coronaviruses in wild birds. Specifically, we explore host range at the levels of viral genus and species, and reveal the multi-host nature of many viral species, albeit with biases to certain types of avian host. We conclude that it is currently challenging to infer viral ecology due to major sampling and technical limitations, and suggest that improved assay performance across the breadth of gamma- and deltacoronaviruses, assay standardization, as well as better sequencing approaches, will improve both the repeatability and interpretation of results. Finally, we discuss cross-species virus transmission across both the wild bird - poultry interface as well as from birds to mammals. Clarifying the ecology and diversity in the wild bird reservoir has important ramifications for our ability to respond to the likely future emergence of coronaviruses in socioeconomically important animal species or human populations.

Association of insularity and body condition to cloacal bacteria prevalence in a small shorebird

Do islands harbour less diverse disease communities than mainland? The island biogeography theory predicts more diverse communities on mainland than on islands due to more niches, more diverse habitats and availability of greater range of hosts. We compared bacteria prevalences of Campylobacter, Chlamydia and Salmonella in cloacal samples of a small shorebird, the Kentish plover (Charadrius alexandrinus) between two island populations of Macaronesia and two mainland locations in the Iberian Peninsula. Bacteria were found in all populations but, contrary to the expectations, prevalences did not differ between islands and mainland. Females had higher prevalences than males for Salmonella and when three bacteria genera were pooled together. Bacteria infection was unrelated to bird’s body condition but females from mainland were heavier than males and birds from mainland were heavier than those from islands. Abiotic variables consistent throughout breeding sites, like high salinity that is known to inhibit bacteria growth, could explain the lack of differences in the bacteria prevalence between areas. We argue about the possible drivers and implications of sex differences in bacteria prevalence in Kentish plovers.

Salmonellosis in Hedgehogs

African pygmy hedgehogs are popular pets worldwide. The knowledge and understanding of pet hedgehog common veterinary conditions are increasing as new information and research are published; however, there is still much to learn about this fascinating animal. Salmonella is one of the most common zoonoses worldwide and is naturally isolated from the intestinal tract of many animal species, including hedgehogs. This article discusses the cause, clinical signs, diagnosis, treatment, and prevention of salmonella infection in hedgehogs, primarily focusing on African pygmy hedgehogs, with some reference to European hedgehogs.

Evidence of the role of free-living birds as disseminators of Salmonella spp

ABSTRACT This study aimed to review aspects of Salmonella spp. in free-living birds and their potential as disseminators for domestic animals, man, and the environment. Isolation of Salmonella spp. have been reported in several species of wild birds from Passeridae and Fringillidae, among other avian families, captured in countries of North America and Europe, where Salmonella ser. Typhimurium is the most frequently reported serotype. The presence of pathogens, including Salmonella, may be influenced by several factors, such as diet, environment, exposure to antibiotics, infection by pathogenic organisms and migration patterns. Researches with wild birds that live in urbanized environment are important, considering that birds may participate in the transmission of zoonotic pathogens, which are more prevalent in cities due to the human activity. Based on the information collected, this article concludes that wild birds are still important disseminators of pathogens in several geographic regions and may affect man, domestic animals, and other birds.

Salmonella in Retail Food and Wild Birds in Singapore-Prevalence, Antimicrobial Resistance, and Sequence Types

Non-typhoidal salmonellosis is a leading cause of foodborne zoonosis. To better understand the epidemiology of human salmonellosis, this study aimed to determine the prevalence, antimicrobial resistance and sequence types of Salmonella in retail food and wild birds (proximity to humans) in Singapore. We analyzed 21,428 cooked and ready-to-eat food and 1,510 residual faecal samples of wild birds collected during 2010–2015. Thirty-two Salmonella isolates from food and wild birds were subjected to disc diffusion and multi-locus sequence typing (MLST). Salmonella was isolated from 0.08% (17/21,428) of food and 0.99% (15/1510) of wild birds. None of the isolates from wild birds (n = 15) exhibited phenotypic resistance, while the isolates from food (47.1%, 8/17) showed a high prevalence of phenotypic resistance to, at least, one antimicrobial. These findings suggested that the avian Salmonella isolates had been subjected to less antimicrobial selection pressure than those from food samples. MLST revealed specific sequence types found in both food and wild birds. The study can guide future studies with whole-genome analysis on a larger number of isolates from various sectors for public health measures.

A review of Salmonella enterica with particular focus on the pathogenicity and virulence factors, host specificity and antimicrobial resistance including multidrug resistance

Salmonella genus represents the most common foodborne pathogens frequently isolated from food-producing animals that is responsible for zoonotic infections in humans and animal species including birds. Thus, Salmonella infections represent a major concern to public health, animals, and food industry worldwide. Salmonella enterica represents the most pathogenic specie and includes > 2600 serovars characterized thus far. Salmonella can be transmitted to humans along the farm-to-fork continuum, commonly through contaminated foods of animal origin, namely poultry and poultry-related products (eggs), pork, fish etc. Some Salmonella serovars are restricted to one specific host commonly referred to as "host-restricted" whereas others have broad host spectrum known as "host-adapted" serovars. For Salmonella to colonize its hosts through invading, attaching, and bypassing the host's intestinal defense mechanisms such as the gastric acid, many virulence markers and determinants have been demonstrated to play crucial role in its pathogenesis; and these factors included flagella, capsule, plasmids, adhesion systems, and type 3 secretion systems encoded on the Salmonella pathogenicity island (SPI)-1 and SPI-2, and other SPIs. The epidemiologically important non-typhoidal Salmonella (NTS) serovars linked with a high burden of foodborne Salmonella outbreaks in humans worldwide included Typhimurium, Enteritidis, Heidelberg, and Newport. The increased number of NTS cases reported through surveillance in recent years from the United States, Europe and low- and middle-income countries of the world suggested that the control programs targeted at reducing the contamination of food animals along the food chain have largely not been successful. Furthermore, the emergence of several clones of Salmonella resistant to multiple antimicrobials worldwide underscores a significant food safety hazard. In this review, we discussed on the historical background, nomenclature and taxonomy, morphological features, physical and biochemical characteristics of NTS with a particular focus on the pathogenicity and virulence factors, host specificity, transmission, and antimicrobial resistance including multidrug resistance and its surveillance.

Health hazards to wild birds and risk factors associated with anthropogenic food provisioning

Provision of supplementary food for wild birds at garden feeding stations is a common, large-scale and year-round practice in multiple countries including Great Britain (GB). While these additional dietary resources can benefit wildlife, there is a concomitant risk of disease transmission, particularly when birds repeatedly congregate in the same place at high densities and through interactions of species that would not normally associate in close proximity. Citizen science schemes recording garden birds are popular and can integrate disease surveillance with population monitoring, offering a unique opportunity to explore inter-relationships between supplementary feeding, disease epidemiology and population dynamics. Here, we present findings from a national surveillance programme in GB and note the dynamism of endemic and emerging diseases over a 25-year period, focusing on protozoal (finch trichomonosis), viral (Paridae pox) and bacterial (passerine salmonellosis) diseases with contrasting modes of transmission. We also examine the occurrence of mycotoxin contamination of food residues in bird feeders, which present both a direct and indirect (though immunosuppression) risk to wild bird health. Our results inform evidence-based mitigation strategies to minimize anthropogenically mediated health hazards, while maintaining the benefits of providing supplementary food for wild birds.This article is part of the theme issue 'Anthropogenic resource subsidies and host-parasite dynamics in wildlife'.

Assessing the contributions of intraspecific and environmental sources of infection in urban wildlife: Salmonella enterica and white ibis as a case study

Conversion of natural habitats into urban landscapes can expose wildlife to novel pathogens and alter pathogen transmission pathways. Because transmission is difficult to quantify for many wildlife pathogens, mathematical models paired with field observations can help select among competing transmission pathways that might operate in urban landscapes. Here we develop a mathematical model for the enteric bacteria Salmonella enterica in urban-foraging white ibis ( Eudocimus albus) in south Florida as a case study to determine (i) the relative importance of contact-based versus environmental transmission among ibis and (ii) whether transmission can be supported by ibis alone or requires external sources of infection. We use biannual field prevalence data to restrict model outputs generated from a Latin hypercube sample of parameter space and select among competing transmission scenarios. We find the most support for transmission from environmental uptake rather than between-host contact and that ibis-ibis transmission alone could maintain low infection prevalence. Our analysis provides the first parameter estimates for Salmonella shedding and uptake in a wild bird and provides a key starting point for predicting how ibis response to urbanization alters their exposure to a multi-host zoonotic enteric pathogen. More broadly, our study provides an analytical roadmap to assess transmission pathways of multi-host wildlife pathogens in the face of scarce infection data.

Diversity of Salmonella serotypes from humans, food, domestic animals and wildlife in New South Wales, Australia

BACKGROUND

Salmonella is an important human pathogen in Australia and annual case rates continue to increase. In addition to foodborne exposures, cases have been associated with animal and contaminated environment contact. However, routine surveillance in Australia has tended to focus on humans and food, with no reported attempts to collate and compare Salmonella data from a wider range of potential sources of exposure.

METHODS

Salmonella data from humans, food, animals and environments were collated from a range of surveillance and diagnostic sources in New South Wales (NSW). Data were categorised to reflect one of 29 sample origins. Serotype diversity was described for each category, and the distribution of serotypes commonly isolated from humans was examined for each sample origin. The distribution of serotypes along the livestock-food-human continuum and at the companion animal-wildlife interface was also examined.

RESULTS

In total, 49,872 Salmonella isolates were included in this analysis, comprising 325 serotypes. The vast majority of these isolates were from humans (n = 38,106). Overall S. Typhimurium was the most frequently isolated serotype and was isolated from all sample categories except natural environment and game meat. S. Enteriditis was not isolated from any livestock animal, however sporadic cases were documented in food, companion animals and a reptile. Many serotypes that were frequently isolated from livestock animals and associated food products were only rarely isolated from humans. In addition, a number of key human serotypes were only sporadically isolated from livestock and food products, suggesting alternative sources of infection. In particular, S. Paratyphi B Java and S. Wangata were more often isolated from wild animals. Finally, there was some overlap between serotypes in companion animals and wildlife, with cats in particular having a large number of serotypes in common with wild birds.

CONCLUSIONS

This is the most comprehensive description of Salmonella data from humans, food, livestock, wildlife, companion animals and various environments in Australia reported to date. Results confirm that livestock and food are important sources of salmonellosis in humans but that alternative sources - such as contact with wildlife and environments - warrant further investigation. Surveillance in NSW is largely human-focussed: major knowledge gaps exist regarding the diversity and frequency of serotypes in animals. More systematic surveillance of domestic animals and wildlife is needed to inform targeted control strategies and quantitative source attribution modelling in this state.

RECENT CHANGES IN INFECTIOUS DISEASES IN EUROPEAN WILDLIFE

Many infectious diseases originating from, or carried by, wildlife affect wildlife conservation and biodiversity, livestock health, or human health. We provide an update on changes in the epidemiology of 25 selected infectious, wildlife-related diseases in Europe (from 2010-16) that had an impact, or may have a future impact, on the health of wildlife, livestock, and humans. These pathogens were selected based on their: 1) identification in recent Europe-wide projects as important surveillance targets, 2) inclusion in European Union legislation as pathogens requiring obligatory surveillance, 3) presence in recent literature on wildlife-related diseases in Europe since 2010, 4) inclusion in key pathogen lists released by the Office International des Epizooties, 5) identification in conference presentations and informal discussions on a group email list by a European network of wildlife disease scientists from the European Wildlife Disease Association, or 6) identification as pathogens with changes in their epidemiology during 2010-16. The wildlife pathogens or diseases included in this review are: avian influenza virus, seal influenza virus, lagoviruses, rabies virus, bat lyssaviruses, filoviruses, canine distemper virus, morbilliviruses in aquatic mammals, bluetongue virus, West Nile virus, hantaviruses, Schmallenberg virus, Crimean-Congo hemorrhagic fever virus, African swine fever virus, amphibian ranavirus, hepatitis E virus, bovine tuberculosis ( Mycobacterium bovis), tularemia ( Francisella tularensis), brucellosis ( Brucella spp.), salmonellosis ( Salmonella spp.), Coxiella burnetii, chytridiomycosis, Echinococcus multilocularis, Leishmania infantum, and chronic wasting disease. Further work is needed to identify all of the key drivers of disease change and emergence, as they appear to be influencing the incidence and spread of these pathogens in Europe. We present a summary of these recent changes during 2010-16 to discuss possible commonalities and drivers of disease change and to identify directions for future work on wildlife-related diseases in Europe. Many of the pathogens are entering Europe from other continents while others are expanding their ranges inside and beyond Europe. Surveillance for these wildlife-related diseases at a continental scale is therefore important for planet-wide assessment, awareness of, and preparedness for the risks they may pose to wildlife, domestic animal, and human health.

Retracted: Antibiotic Resistance in Salmonella Enteritidis Isolates Recovered from Chicken, Chicken Breast, and Humans Through National Antimicrobial Resistance Monitoring System Between 1996 and 2014

The online e-pub version of the article entitled, Antibiotic Resistance in Salmonella Enteritidis Isolates Recovered from Chicken, Chicken Breast, and Humans Through National Antimicrobial Resistance Monitoring System Between 1996 and 2014" by Paudyal N, Pan H, Li X. Fang W. Yue M., Foodborne Pathog Dis [Epub ahead of print]; DOI: 10.1089/fpd.2017.2402 is being officially retracted from Foodborne Pathogens and Disease (FPD) due to a significant number of errors in reporting and miscalculations of the National Antimicrobial Resistance Monitoring System (NARMS) datasets reported in the paper. Authors evaluated NARMS data, which are in the public domain, and analyzed a subset of NARMS data to address questions about a specific serotype of Salmonella in humans and chicken meat. Authors analyzed Salmonella Enteritidis isolates from humans, chicken and retail chicken meat, with their minimum inhibitory concentrations (MICs) to a range of commonly used antibiotics in the US collected over a period of 1996-2014 by NARMS, to segregate isolates based on their MIC value for a certain antimicrobial and evaluate their relationship along the foodborne transmission pathway. NARMS has data on more than 185,000 isolates that can be downloaded in an accessible format. To help make these large data sets more accessible, the NARMS teams continue to develop new tools to enable users to explore them according to their own interests. As a public health surveillance system, the goal is continuous improvement and open, transparent data sharing. The NARMS partners believe this is the best way to foster a collaborative effort to combat antibiotic resistance. After the online-ahead-of-print version of the paper, which used a subset of NARMS data, was published, a significant concern was brought to the attention of the Editor-in-Chief of FPD indicating that the article contained several significant errors which could potentially lead to a misunderstanding of the resistance situation in the United States. Of particular import is with regard to the authors of the paper reversing the poultry and human resistance data found in Figure 2, which displays the overall antimicrobial resistance data and is a central element of the article. The authors correctly state it in the text, but the figure is incorrect. Additionally, there appeared to be an accidental omission of a reference to a published article which shows a strong association between quinolone-resistant Salmonella Enteritidis infections in humans and international travel (O'Donnell et al., 2014) This appears to be a critical oversight given that the intention of the study was to analyze the NARMS data to help understand the dynamics of Salmonella transmission. The authors of the published article were notified of this communication by the Editor of FPD and were provided an opportunity to respond, which they quickly did. The corresponding author, Dr. Min Yue, agreed that after he and his team reanalyzed the data, there were indeed errors in the published paper and supplied revised versions of Figure 2 and supplemental Figure 3, as well as providing a significantly revised version of the manuscript, based upon the criticisms levied against the published paper. After giving the revised manuscript and figures very careful consideration, and after significant probing of his own, the Editor of FPD determined that the significantly revised manuscript, coupled with the multiple errors presented in the figures, is simply far too weighty for a correction statement to be issued, and determined a full retraction of the published article was warranted. It is important to note that there is no indication whatsoever that the errors or miscalculations were intentional, and that Dr. Yue and his team quickly and honestly replied to the concerns raised about their work. However, in the interest of upholding the proper protocols of peer review, and in accurate and truthful reporting in the scientific literature, the Editor of Foodborne Pathogens and Diseases is issuing this full and formal retraction of the article.

Genome Variation and Molecular Epidemiology of Salmonella enterica Serovar Typhimurium Pathovariants

Salmonella enterica serovar Typhimurium is one of approximately 2,500 distinct serovars of the genus Salmonella but is exceptional in its wide distribution in the environment, livestock, and wild animals. S Typhimurium causes a large proportion of nontyphoidal Salmonella (NTS) infections, accounting for a quarter of infections, second only to S. enterica serovar Enteritidis in incidence. S Typhimurium was once considered the archetypal broad-host-range Salmonella serovar due to its wide distribution in livestock and wild animals, and much of what we know of the interaction of Salmonella with the host comes from research using a small number of laboratory strains of the serovar (LT2, SL1344, and ATCC 14028). But it has become clear that these strains do not reflect the genotypic or phenotypic diversity of S Typhimurium. Here, we review the epidemiological record of S Typhimurium and studies of the host-pathogen interactions of diverse strains of S Typhimurium. We present the concept of distinct pathovariants of S Typhimurium that exhibit diversity of host range, distribution in the environment, pathogenicity, and risk to food safety. We review recent evidence from whole-genome sequencing that has revealed the extent of genomic diversity of S Typhimurium pathovariants, the genomic basis of differences in the level of risk to human and animal health, and the molecular epidemiology of prominent strains. An improved understanding of the impact of genome variation of bacterial pathogens on pathogen-host and pathogen-environment interactions has the potential to improve quantitative risk assessment and reveal how new pathogens evolve.

Differential Distribution of Salmonella Serovars and Campylobacter spp. Isolates in Free-Living Crows and Broiler Chickens in Aomori, Japan

Salmonella and Campylobacter cause foodborne enteritis mainly via the consumption of raw/undercooked contaminated poultry meat and products. Broiler flocks are primarily colonized with these bacteria; however, the underlying etiology remains unclear. The present study was conducted in order to obtain further information on the prevalence and genotypic distribution of Salmonella and Campylobacter in free-living crows and broiler flocks in a region for 2 years, thereby facilitating estimations of the potential risk of transmission of C. jejuni from crows to broiler flocks. Salmonella serovars Bredeney and Derby were isolated from 8 and 3 out of 123 captured crows, respectively, both of which are not common in broiler chickens. Campylobacter were isolated from all 89 crows tested and C. jejuni was prevalent (85 crows). Pulsed field gel electrophoresis showed broad diversity in the crow isolates of C. jejuni. However, 3 crow isolates and 2 broiler isolates showing similar banding patterns were assigned to different sequence types in multi-locus sequence typing. These results indicate that crows do not share Salmonella serovars with broilers, and harbor various genotypes of C. jejuni that differ from those of broiler flocks. Thus, our results indicate that crows are not a potential vector of these bacteria to broiler flocks in this region.

Salmonella Enteritidis ST183: emerging and endemic biotypes affecting western European hedgehogs (Erinaceus europaeus) and people in Great Britain

The impacts of hedgehog (Erinaceus europaeus) Salmonella infection on public health and on animal welfare and conservation are unknown. We isolated Salmonella Enteritidis multi-locus sequence-type (ST)183 from 46/170 (27%) hedgehog carcasses (27 S. Enteritidis phage type (PT)11, 18 of a novel PT66 biotype and one with co-infection of these PTs) and from 6/208 (3%) hedgehog faecal samples (4 PT11, 2 PT66) from across Great Britain, 2012–2015. Whole genome phylogenetic analysis of the hedgehog isolates and ST183 from people in England and Wales found that PT11 and PT66 form two divergent clades. Hedgehog and human isolates were interspersed throughout the phylogeny indicating that infections in both species originate from a common population. PT11 was recovered from hedgehogs across England and Scotland, consistent with endemic infection. PT66 was isolated from Scotland only, possibly indicating a recent emergence event. People infected with ST183 were four times more likely to be aged 0–4 years than people infected by the more common ST11 S. Enteritidis. Evidence for human ST183 infection being non-foodborne included stronger correlation between geographic and genetic distance, and significantly increased likelihood of infection in rural areas, than for ST11. These results are consistent with hedgehogs acting as a source of zoonotic infection.

Free-Ranging Synanthropic Birds (Ardea alba and Columba livia domestica) as Carriers of Salmonella spp. and Diarrheagenic Escherichia coli in the Vicinity of an Urban Zoo

The presence of free-ranging urban birds is a risk factor for transmitting pathogens to captive animals and humans alike, including Salmonella spp. and diarrheagenic Escherichia coli. Cloacal swabs from 156 synanthropic Great egrets (Ardea alba) and feral pigeons (Columba livia domestica) that inhabit the surroundings of an urban zoo were processed for the identification of Salmonella spp. and diarrheagenic E. coli pathotypes. Bacterial species identification and genotypic characterization employed the matrix-assisted laser desorption ionization-time of flight mass spectrometry and PCR techniques, respectively, comparing their phylogenetic profiles through amplified fragment length polymorphism (AFLP) analysis. A total of 11 birds were positive for Salmonella Typhimurium (7%) and 9 individuals (5.8%) for diarrheagenic E. coli (enteropathogenic E. coli/Shiga-toxin producing E. coli [EPEC/STEC]) strains. S. Typhimurium strains presented highly similar AFLP profiles (85-100%), whereas EPEC/STEC strains showed more polymorphism. The results show free-ranging birds as carriers for both microorganisms in a zoo environment in Brazil for the first time and suggest these species as possible sources of infection to other animals as well as exposing personnel and visitors to potential zoonotic microorganisms. The presence of carriers highlights the importance of a surveillance system and the need for preventive measures to avoid attracting growing number of synanthropic avian species.

Estimates of the burden of illness for eight enteric pathogens associated with animal contact in Canada

Enteric pathogens are commonly known to be transmitted through food or water; however, contact with animals is another important transmission route. This study estimated the annual burden of illness attributable to animal contact for eight enteric pathogens in Canada. Using data from a Canadian expert elicitation on transmission routes, the proportion of enteric illnesses attributable to animal contact was estimated for each pathogen to estimate the annual number of illnesses, hospitalizations and deaths in Canada. For each estimate, a mean and probability intervals were generated. Of all illnesses caused by these eight pathogens, 16% were estimated attributable to animal contact. This estimate translates to 86 000 (31 000–166 000) illnesses, 488 (186–890) hospitalizations and 12 (2–28) deaths annually for the eight pathogens combined. Campylobacter spp. is the leading cause of illnesses annually, with an estimated 38 000 (14 000–71 000) illnesses occurring each year, followed by non-typhoidal Salmonella spp. (17 000, 6000–32 000). The majority of hospitalizations were attributable to non-typhoidal Salmonella spp. (36%) and Campylobacter spp. (31%). Non-typhoidal Salmonella spp. (28%) and Listeria monocytogenes (31%) were responsible for the majority of the estimated deaths. These results identify farm animal and pet/pet food exposure as key pathways of transmission for several pathogens. The estimated burden of illness associated with animal contact is substantial.

Urbanization and Disease Emergence: Dynamics at the Wildlife-Livestock-Human Interface

Urbanization is characterized by rapid intensification of agriculture, socioeconomic change, and ecological fragmentation, which can have profound impacts on the epidemiology of infectious disease. Here, we review current scientific evidence for the drivers and epidemiology of emerging wildlife-borne zoonoses in urban landscapes, where anthropogenic pressures can create diverse wildlife-livestock-human interfaces. We argue that these interfaces represent a critical point for cross-species transmission and emergence of pathogens into new host populations, and thus understanding their form and function is necessary to identify suitable interventions to mitigate the risk of disease emergence. To achieve this, interfaces must be studied as complex, multihost communities whose structure and form are dictated by both ecological and anthropological factors.

Genomic Analysis of Salmonella enterica Serovar Typhimurium from Wild Passerines in England and Wales

Passerine salmonellosis is a well-recognized disease of birds in the order Passeriformes, which includes common songbirds such as finches and sparrows, caused by infection with Salmonella enterica serovar Typhimurium. Previous research has suggested that some subtypes of S Typhimurium-definitive phage types (DTs) 40, 56 variant, and 160-are host adapted to passerines and that these birds may represent a reservoir of infection for humans and other animals. Here, we have used the whole-genome sequences of 11 isolates from British passerines, five isolates of similar DTs from humans and a domestic cat, and previously published S Typhimurium genomes that include similar DTs from other hosts to investigate the phylogenetic relatedness of passerine salmonellae to other S Typhimurium isolates and investigate possible genetic features of the distinct disease pathogenesis of S Typhimurium in passerines. Our results demonstrate that the 11 passerine isolates and 13 other isolates, including those from nonpasserine hosts, were genetically closely related, with a median pairwise single nucleotide polymorphism (SNP) difference of 130 SNPs. These 24 isolates did not carry antimicrobial resistance genetic determinants or the S Typhimurium virulence plasmid. Although our study does not provide evidence of Salmonella transmission from passerines to other hosts, our results are consistent with the hypothesis that wild birds represent a potential reservoir of these Salmonella subtypes, and thus, sensible personal hygiene precautions should be taken when feeding or handling garden birds.

IMPORTANCE

Passerine salmonellosis, caused by certain definitive phage types (DTs) of Salmonella Typhimurium, has been documented as a cause of wild passerine mortality since the 1950s in many countries, often in the vicinity of garden bird feeding stations. To gain better insight into its epidemiology and host-pathogen interactions, we sequenced the genomes of a collection of 11 isolates from wild passerine salmonellosis in England and Wales. Phylogenetic analysis showed these passerine isolates to be closely related to each other and to form a clade that is distinct from other strains of S Typhimurium, which included a multidrug-resistant isolate from invasive nontyphoidal Salmonella disease that shares the same phage type as several of the passerine isolates. Closely related to wild passerine isolates and within the same clade were four S Typhimurium isolates from humans as well as isolates from horses, poultry, cattle, an unspecified wild bird, and a domestic cat and dog with similar DTs and/or multilocus sequence types. This suggests the potential for cross-species transmission, and the genome sequences provide a valuable resource to investigate passerine salmonellosis further.

Urbanized White Ibises (Eudocimus albus) as Carriers of Salmonella enterica of Significance to Public Health and Wildlife

Worldwide, Salmonella spp. is a significant cause of disease for both humans and wildlife, with wild birds adapted to urban environments having different opportunities for pathogen exposure, infection, and transmission compared to their natural conspecifics. Food provisioning by people may influence these factors, especially when high-density mixed species flocks aggregate. White Ibises (Eudocimus albus), an iconic Everglades species in decline in Florida, are becoming increasingly common in urbanized areas of south Florida where most are hand-fed. We examined the prevalence of Salmonella shedding by ibises to determine the role of landscape characteristics where ibis forage and their behavior, on shedding rates. We also compared Salmonella isolated from ibises to human isolates to better understand non-foodborne human salmonellosis. From 2010-2013, 13% (n = 261) adult/subadult ibises and 35% (n = 72) nestlings sampled were shedding Salmonella. The prevalence of Salmonella shedding by ibises significantly decreased as the percent of Palustrine emergent wetlands and herbaceous grasslands increased, and increased as the proportion of open-developed land types (e.g. parks, lawns, golf courses) increased, suggesting that natural ecosystem land cover types supported birds with a lower prevalence of infection. A high diversity of Salmonella serotypes (n = 24) and strain types (43 PFGE types) were shed by ibises, of which 33% of the serotypes ranked in the top 20 of high significance for people in the years of the study. Importantly, 44% of the Salmonella Pulsed-Field Gel Electrophoresis patterns for ibis isolates (n = 43) matched profiles in the CDC PulseNet USA database. Of these, 20% came from Florida in the same three years we sampled ibis. Importantly, there was a negative relationship between the amount of Palustrine emergent wetland and the number of Salmonella isolates from ibises that matched human cases in the PulseNet database (p = 0.056). Together, our results indicate that ibises are good indicators of salmonellae strains circulating in their environment and they have both the potential and opportunity to transmit salmonellae to people. Finally, they may act as salmonellae carriers to natural environments where other more highly-susceptible groups (nestlings) may be detrimentally affected.

Chasing Salmonella Typhimurium in free range egg production system

Free range production systems are becoming a major source of egg production in Australia and worldwide. This study investigated shedding and ecology of Salmonella Typhimurium and Salmonella species in a free range layer flock, wild birds and foxes in the vicinity of the free range farm in different seasons. Shedding of Salmonella was significantly higher in summer. Within the shed, overall, Salmonella prevalence was highest in dust. Corticosterone level in faeces was highest in spring and lowest in winter. There was no direct association between the Salmonella shedding (MPN/gm) and corticosterone levels in faeces. Salmonella Typhimurium MLVA types isolated from fox and wild birds were similar to MLVA types isolated from layer flock and reported during human food borne illness. Wild birds and foxes appear to play an important role in S. Typhimurium ecology and food safety. Environmental factors could play a role in evolution of S. Typhimurium in free range environment.

MORTALITY OF SELECTED AVIAN ORDERS SUBMITTED TO A WILDLIFE DIAGNOSTIC LABORATORY (SOUTHEASTERN COOPERATIVE WILDLIFE DISEASE STUDY, USA): A 36-YEAR RETROSPECTIVE ANALYSIS

To determine the relative importance of mortality factors for birds and to assess for patterns in avian mortality over time, we retrospectively examined data of birds submitted to the Southeastern Cooperative Wildlife Disease Study (SCWDS; http://vet.uga.edu/scwds ), US, from 1976 to 2012. During this period, SCWDS, a wildlife diagnostic laboratory, received 2,583 wild bird specimens, from the taxonomic orders Apodiformes, Caprimulgiformes, Cuculiformes, Passeriformes, and Piciformes, originating from 22 states. Data from 2,001 of these birds were analyzed using log-linear models to explore correlations between causes of mortality, taxonomic family, demography, geographic location, and seasonality. Toxicosis was the major cause of mortality, followed by trauma, bacterial infection, physiologic stress, viral infection, and other (mortality causes with low sample numbers and etiologies inconsistent with established categories). Birds submitted during fall and winter had a higher frequency of parasitic infections, trauma, and toxicoses, whereas birds submitted during the spring and summer were more likely to die of an infectious disease, physiologic stress, or trauma. We noted a decrease in toxicoses concurrent with an increase in bacterial infections and trauma diagnoses after the mid-1990s. Toxicosis was the most commonly diagnosed cause of death among adult birds; the majority of juveniles died from physiologic stress, trauma, or viral infections. Infectious agents were diagnosed more often within the families Cardinalidae and Fringilidae, whereas noninfectious etiologies were the primary diagnoses in the Bombycillidae, Parulidae, Sturnidae, Turdidae, and Icteridae. There are important inherent limitations in the examination of data from diagnostic labs, as submission of cases varies in timing, frequency, location, and species and is often influenced by several factors, including media coverage of high-profile mortality events. Notwithstanding, our data provide a rare opportunity to examine long-term, regional, and temporal patterns in causes of avian mortality, and they allow for the analysis of novel and rare mortality factors.

House Sparrows Do Not Constitute a Significant Salmonella Typhimurium Reservoir across Urban Gradients in Flanders, Belgium

In recent decades major declines in urban house sparrow (Passer domesticus) populations have been observed in north-western European cities, whereas suburban and rural house sparrow populations have remained relatively stable or are recovering from previous declines. Differential exposure to avian pathogens known to cause epidemics in house sparrows may in part explain this spatial pattern of declines. Here we investigate the potential effect of urbanization on the development of a bacterial pathogen reservoir in free-ranging house sparrows. This was achieved by comparing the prevalence of Salmonella enterica subspecies enterica serotype Typhimurium in 364 apparently healthy house sparrows captured in urban, suburban and rural regions across Flanders, Belgium between September 2013 and March 2014. In addition 12 dead birds, received from bird rescue centers, were necropsied. The apparent absence of Salmonella Typhimurium in fecal samples of healthy birds, and the identification of only one house sparrow seropositive for Salmonella spp., suggests that during the winter of 2013–2014 these birds did not represent any considerable Salmonella Typhimurium reservoir in Belgium and thus may be considered naïve hosts, susceptible to clinical infection. This susceptibility is demonstrated by the isolation of two different Salmonella Typhimurium strains from two of the deceased house sparrows: one DT99, typically associated with disease in pigeons, and one DT195, previously associated with a passerine decline. The apparent absence (prevalence: <1.3%) of a reservoir in healthy house sparrows and the association of infection with clinical disease suggests that the impact of Salmonella Typhimurium on house sparrows is largely driven by the risk of exogenous exposure to pathogenic Salmonella Typhimurium strains. However, no inference could be made on a causal relationship between Salmonella infection and the observed house sparrow population declines.

Salmonella infection in grey seals (Halichoerus grypus), a marine mammal sentinel species: pathogenicity and molecular typing of Salmonella strains compared with human and livestock isolates

Microbial pollution of the marine environment through land-sea transfer of human and livestock pathogens is of concern. Salmonella was isolated from rectal swabs of free-ranging and stranded grey seal pups (21.1%; 37/175) and compared with strains from the same serovars isolated from human clinical cases, livestock, wild mammals and birds in Scotland, UK to characterize possible transmission routes using pulsed-field gel electrophoresis and multi-locus variable number of tandem repeat analyses. A higher prevalence of Salmonella was found in pups exposed to seawater, suggesting that this may represent a source of this pathogen. Salmonella Bovismorbificans was the most common isolate (18.3% pups; 32/175) and was indistinguishable from isolates found in Scottish cattle. Salmonella Typhimurium was infrequent (2.3% pups; 4/175), mostly similar to isolates found in garden birds and, in one case, identical to a highly multidrug resistant strain isolated from a human child. Salmonella Haifa was rare (1.1% pups; 2/175), but isolates were indistinguishable from that of a human clinical isolate. These results suggest that S. Bovismorbificans may circulate between grey seal and cattle populations and that both S. Typhimurium and S. Haifa isolates are shared with humans, raising concerns of microbial marine pollution.

Supplementary feeding restructures urban bird communities

Food availability is a primary driver of avian population regulation. However, few studies have considered the effects of what is essentially a massive supplementary feeding experiment: the practice of wild bird feeding. Bird feeding has been posited as an important factor influencing the structure of bird communities, especially in urban areas, although experimental evidence to support this is almost entirely lacking. We carried out an 18-mo experimental feeding study at 23 residential properties to investigate the effects of bird feeding on local urban avian assemblages. Our feeding regime was based on predominant urban feeding practices in our region. We used monthly bird surveys to compare avian community composition, species richness, and the densities of local species at feeding and nonfeeding properties. Avian community structure diverged at feeding properties and five of the commonest garden bird species were affected by the experimental feeding regime. Introduced birds particularly benefitted, with dramatic increases observed in the abundances of house sparrow (Passer domesticus) and spotted dove (Streptopelia chinensis) in particular. We also found evidence of a negative effect on the abundance of a native insectivore, the grey warbler (Gerygone igata). Almost all of the observed changes did not persist once feeding had ceased. Our study directly demonstrates that the human pastime of bird feeding substantially contributes to the structure of avian community in urban areas, potentially altering the balance between native and introduced species.