Reassortant influenza A viruses in wild duck populations: effects on viral shedding and persistence in water

Wild ducks of the genus Anas represent the natural hosts for a large genetic diversity of influenza A viruses. In these hosts, co-infections with different virus genotypes are frequent and result in high rates of genetic reassortment. Recent genomic data have provided information regarding the pattern and frequency of these reassortant viruses in duck populations; however, potential consequences on viral shedding and maintenance in the environment have not been investigated. On the basis of full-genome sequencing, we identified five virus genotypes, in a wild duck population in northwestern Minnesota (USA), that naturally arose from genetic reassortments. We investigated the effects of influenza A virus genotype on the viral shedding pattern in Mallards (Anas platyrhynchos) and the duration of infectivity in water, under different temperature regimens. Overall, we found that variation in the viral genome composition of these isolates had limited effects on duration, extent and pattern of viral shedding, as well as on the reduction of infectivity in water over time. These results support that, in wild ducks, functionally equivalent gene segments could be maintained in virus populations with no fitness costs when genetic reassortments occur.     

Understanding the ecological drivers of avian influenza virus infection in wildfowl: a continental-scale study across Africa

Despite considerable effort for surveillance of wild birds for avian influenza viruses (AIVs), empirical investigations of ecological drivers of AIV prevalence in wild birds are still scarce. Here we used a continental-scale dataset, collected in tropical wetlands of 15 African countries, to test the relative roles of a range of ecological factors on patterns of AIV prevalence in wildfowl. Seasonal and geographical variations in prevalence were positively related to the local density of the wildfowl community and to the wintering period of Eurasian migratory birds in Africa. The predominant influence of wildfowl density with no influence of climatic conditions suggests, in contrast to temperate regions, a predominant role for inter-individual transmission rather than transmission via long-lived virus persisting in the environment. Higher prevalences were found in Anas species than in non-Anas species even when we account for differences in their foraging behaviour (primarily dabbling or not) or their geographical origin (Eurasian or Afro-tropical), suggesting the existence of intrinsic differences between wildfowl taxonomic groups in receptivity to infection. Birds were found infected as often in oropharyngeal as in cloacal samples, but rarely for both types of sample concurrently, indicating that both respiratory and digestive tracts may be important for AIV replication.     

Seasonal changes in the feeding pattern of Culex pipiens pallens govern the transmission dynamics of multiple lineages of avian malaria parasites in Japanese wild bird community

Heterogeneity in the transmission of mosquito-borne pathogens is determined largely by distribution patterns of mosquito bites among wild animal populations. Although mosquitoes are crucial for transmission of avian malaria parasites, little is known about the ecology of natural vectors. We examined bloodmeal and parasite incidence in Culex pipiens pallens by a polymerase chain reaction (PCR)-based procedure to determine how the feeding pattern of mosquitoes govern transmission dynamics of avian malaria parasites in Japanese wild birds. We collected 881 unfed and 486 blood-fed Cx. pipiens pallens resting on vegetation in a park in Tokyo. The mosquitoes were separated into abdomen and thorax prior to PCR screening. Abdomens of unfed mosquitoes were combined into 95 pools. From these, we amplified Plasmodium DNA in 32 (33.7%) pools. Among blood-fed mosquitoes, 371 individuals were screened for blood-sources and Plasmodium parasites. Plasmodium DNA was amplified from mosquitoes fed on 6 of 13 avian species identified as blood-sources. Ten Plasmodium lineages were identified on the basis of 478 bp of the cytochrome b gene, with 0.2-10% sequence divergence. The three commonest Plasmodium lineages (CXPIP09, SGS1 and PADOM02) were detected in both the abdomens and thoraxes of mosquitoes, strongly suggesting transmission of these lineages. Jungle crow (Corvus macrorhynchos) served as a natural host for the three commonest Plasmodium lineages and made up 63.8% of blood-sources. As a significant increase in feeding of vector mosquitoes on jungle crows coincided with their breeding season, jungle crows were considered to be the primary reservoir of Plasmodium transmission in this study.     

Health of Antarctic birds: a review of their parasites,pathogens and diseases

Antarctic birds are not beyond the effects of parasites or pathogens. However, potential ecological consequences of wide-spread infections for bird populations in Antarctica have received little attention. In this paper, we review the information published about disease and parasites, and their effects on Antarctic birds. The information on host species, parasites and pathogens, and geographic regions is incomplete and data on ecological effects on the populations, including how birds respond to pathogens and parasites, are almost inexistent. We conclude that more research is needed to establish general patterns of spatial and temporal variation in pathogens and parasites, and to determine how such patterns could influence hosts. This information is crucial to limit the spread of outbreaks and may aid in the decision-making process should they occur.     

季节性流感病毒与其他病原混合或继发感染的研究进展与思考

流感病毒包括甲(A)、乙(B)、丙(C)和丁(D)四种型。人流行性感冒是由甲型和乙型季节性流感病毒引起的一种急性呼吸道传染病。流感病毒感染患者主要表现出呼吸道症状,严重时可以导致肺炎。此外,与其他病毒、细菌和支原体等病原体混合或继发感染时,会增加流感患者的重症率和死亡率。近几年,流感病毒与其他病原协同感染的病例有增加趋势。本文归纳总结了流感病毒与其他病原混合及继发感染的研究现状,希望为流感病毒复杂感染情况的临床诊断和治疗方案的制定提供线索。     

The effects of a wind farm on birds in a migration point: the Strait of Gibraltar

The interaction between birds and wind turbines is an important factor to consider when a wind farm is constructed. A wind farm and two control areas were studied in Tarifa (Andalusia Province, southern Spain, 30STF590000–30STE610950). Variables were studied along linear transects in each area and observations of flight were also recorded from fixed points in the wind farm. The main purpose of our research was to determine the impact and the degree of flight behavioural change in birds flights resulting from a wind farm. Soaring birds can detect the presence of the turbines because they change their flight direction when they fly near the turbines and their abundance did not seem to be affected. This is also supported by the low amount of dead birds we found in the whole study period in the wind farm area. More studies will be necessary after and before the construction of wind farms to assess changes in passerine populations. Windfarms do not appear to be more detrimental to birds than other man-made structures.     

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 43772^T, 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 51478^T. 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-H8^T, faydin-H23^T and their close neighbors H. anseris MIT 04-9362^T and H. pametensis ATCC 51478^T, respectively, confirmed that both strains represent novel species in the genus Helicobacter. The DNA G+C contents of the strains faydin-H8^T and faydin-H23^T 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-H8^T(=LMG 32237^T = DSM 112312^T) and faydin-H23^T(=LMG 32236^T = CECT 30508^T) as respective type strains.     

Characterization of H5N6 highly pathogenic avian influenza viruses isolated from wild and captive birds in the winter season of 2016–2017 in Northern Japan

On 15 November 2016, a black swan that had died in a zoo in Akita prefecture, northern Japan, was strongly suspected to have highly pathogenic avian influenza (HPAI); an HPAI virus (HPAIV) belonging to the H5N6 subtype was isolated from specimens taken from the bird. After the initial report, 230 cases of HPAI caused by H5N6 viruses from wild birds, captive birds, and domestic poultry farms were reported throughout the country during the winter season. In the present study, 66 H5N6 HPAIVs isolated from northern Japan were further characterized. Phylogenetic analysis of the hemagglutinin gene showed that the H5N6 viruses isolated in northern Japan clustered into Group C of Clade 2.3.4.4 together with other isolates collected in Japan, Korea and Taiwan during the winter season of 2016–2017. The antigenicity of the Japanese H5N6 isolate differed slightly from that of HPAIVs isolated previously in Japan and China. The virus exhibited high pathogenicity and a high replication capacity in chickens, whereas virus growth was slightly lower in ducks compared with that of an H5N8 HPAIV isolate collected in Japan in 2014. Comprehensive analyses of Japanese isolates, including those from central, western, and southern Japan, as well as rapid publication of this information are essential for facilitating greater control of HPAIVs.

     

Cytokine secretion by stimulated monocytes depends on the growth phase and heat treatment of bacteria: a comparative study between lactic acid bacteria and invasive pathogens

The consumption of food containing lactic acid bacteria (LAB) has been shown to exert immunomodulatory effects in humans. The specific cellular interaction of these bacteria with immuno-competent cells has not yet been fully understood. Since the TNF-alpha secretion of stimulated monocytes is an important initial response to a bacterial challenge, we investigated the potential of LAB originating from the human intestine or fermented food in comparison to the effect of invasive pathogens. The challenge of monocytes with three LAB strains, Listeria monocytogenes or enterohaemorrhagic Escherichia coli (EHEC) elicited a strain specific, dose-dependent biphasic TNF-alpha secretion. The concentration (EDmax) of bacteria or bacterial cell wall components necessary to induce maximal TNF-alpha secretion (TNFmax) by monocytes was mathematically approximated. It was shown for exponentially growing LAB strains that the maximal TNF-alpha secretion (TNFmax) was stronger (57 to 78%) upon stimulation with living bacteria than with heat killed cells. In contrast to log-phase bacteria, the maximal TNF-alpha secretion of monocytes (TNFmax) was higher (15 to 55%) after the stimulation with heat killed, stationary-phase bacteria when compared to that of live LAB. Thus, monocyte stimulation was clearly affected by the growth phase of bacteria. Purified cell walls of LAB strains revealed only a limited potential for monocyte stimulation. LPS exhibited a higher capacity to stimulate monocytes than purified gram positive cell walls or muramyldipeptide. In comparison to pathogenic bacteria, the maximal secretory TNF-alpha response (TNFmax) was up to 2 fold higher with LAB strains. In general, the amount of bacteria (EDmax) necessary to induce maximal TNF-alpha secretion (TNFmax) was approximately 1 to 3 log higher for heat killed bacteria when compared to live bacterial cells illustrating the significant lower potential of heat killed bacteria to activate monocytes.     

Barcoding Neotropical birds: assessing the impact of nonmonophyly in a highly diverse group

In this study, we verified the power of DNA barcodes to discriminate Neotropical birds using Bayesian tree reconstructions of a total of 7404 COI sequences from 1521 species, including 55 Brazilian species with no previous barcode data. We found that 10.4% of species were nonmonophyletic, most likely due to inaccurate taxonomy, incomplete lineage sorting or hybridization. At least 0.5% of the sequences (2.5% of the sampled species) retrieved from GenBank were associated with database errors (poor‐quality sequences, NuMTs, misidentification or unnoticed hybridization). Paraphyletic species (5.8% of the total) can be related to rapid speciation events leading to nonreciprocal monophyly between recently diverged sister species, or to absence of synapomorphies in the small COI region analysed. We also performed two series of genetic distance calculations under the K2P model for intraspecific and interspecific comparisons: the first included all COI sequences, and the second included only monophyletic taxa observed in the Bayesian trees. As expected, the mean and median pairwise distances were smaller for intraspecific than for interspecific comparisons. However, there was no precise ‘barcode gap’, which was shown to be larger in the monophyletic taxon data set than for the data from all species, as expected. Our results indicated that although database errors may explain some of the difficulties in the species discrimination of Neotropical birds, distance‐based barcode assignment may also be compromised because of the high diversity of bird species and more complex speciation events in the Neotropics.     

Haemoplasmas in wild rodents: Routes of transmission and infection dynamics

The way that some parasites and pathogens persist in the hostile environment of their host for long periods remains to be resolved. Here, longitudinal field surveys were combined with laboratory experiments to investigate the routes of transmission and infection dynamics of such a pathogen—a wild rodent haemotropic bacterium, specifically a Mycoplasma haemomuris‐like bacterium. Fleaborne transmission, direct rodent‐to‐rodent transmission and vertical transmission from fleas or rodents to their offspring were experimentally quantified, and indications were found that the main route of bacterial transmission is direct, although its rate of successful transmission is low (~20%). The bacterium's temporal dynamics was then compared in the field to that observed under a controlled infection experiment in field‐infected and laboratory‐infected rodents, and indications were found, under all conditions, that the bacterium reached its peak infection level after 25–45 days and then decreased to low bacterial loads, which persist for the rodent's lifetime. These findings suggest that the bacterium relies on persistency with low bacterial loads for long‐term coexistence with its rodent host, having both conceptual and applied implications.     

Extra pair paternity in birds: a review of interspecific variation and adaptive function

The application of molecular genetic techniques has revolutionized our view of avian mating systems. Contrary to prior expectations, birds are only very rarely sexually monogamous, with 'extra-pair offspring' found in approximately 90% of species. Even among socially monogamous species, over 11% of offspring are, on average, the result of extra-pair paternity (EPP). Based on over 150 molecular genetic studies of EPP in birds, we review two topical areas: (i) ecological explanations for interspecific variation in the rate of EPP; and (ii) evidence bearing on the adaptive function of EPP. We highlight the remaining challenges of understanding the relative roles of genes and ecology in determining variation between taxa in the rate of extra paternity, and testing for differences between extra-pair offspring and those sired within-pair.     

黄瓜霜霉病及寄主抗性机制研究进展

在黄瓜生产中,由古巴假霜霉菌(Pseudoperonospora cubensis)引起的霜霉病危害严重,影响叶、茎和花序生长发育,导致黄瓜产量及品质降低。通过对黄瓜霜霉病的病原菌检测和防御途径、影响及调控因素、抗病原菌候选基因发掘、蛋白质组和基因组分析、黄瓜霜霉病QTL连锁标记开发及其抗病育种等多方面的最新进展进行综述,以期为今后进一步揭示黄瓜乃至农作物对霜霉病的抗性机制研究提供借鉴和参考。     

Microbial contamination of fruit and vegetables and the behaviour of enteropathogens in the phyllosphere: a review

Consumption of fruit and vegetable products is commonly viewed as a potential risk factor for infection with enteropathogens such as Salmonella and Escherichia coli O157, with recent outbreaks linked to lettuce, spinach and tomatoes. Routes of contamination are varied and include application of organic wastes to agricultural land as fertilizer, contamination of waters used for irrigation with faecal material, direct contamination by livestock, wild animals and birds and postharvest issues such as worker hygiene. The ability of pathogens to survive in the field environment has been well studied, leading to the implementation of guidelines such as the Safe Sludge Matrix, which aim to limit the likelihood of viable pathogens remaining at point-of-sale. The behaviour of enteropathogens in the phyllosphere is a growing field of research, and it is suggested that inclusion in phyllosphere biofilms or internalization within the plant augments the survival. Improved knowledge of plant-microbe interactions and the interaction between epiphytic and immigrant micro-organisms on the leaf surface will lead to novel methods to limit enteropathogen survival in the phyllosphere.