Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis

Background

Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes in its genome related to the various steps in the infective process, drug resistance and mobile genetic elements.

Results

For acid and bile resistance, L. hongkongensis possessed a urease gene cassette, two arc gene clusters and bile salt efflux systems. For intestinal colonization, it possessed a putative adhesin of the autotransporter family homologous to those of diffusely adherent Escherichia coli (E. coli) and enterotoxigenic E. coli. To evade from host defense, it possessed superoxide dismutase and catalases. For lipopolysaccharide biosynthesis, it possessed the same set of genes that encode enzymes for synthesizing lipid A, two Kdo units and heptose units as E. coli, but different genes for its symmetrical acylation pattern, and nine genes for polysaccharide side chains biosynthesis. It contained a number of CDSs that encode putative cell surface acting (RTX toxin and hemolysins) and intracellular cytotoxins (patatin-like proteins) and enzymes for invasion (outer membrane phospholipase A). It contained a broad variety of antibiotic resistance-related genes, including genes related to β-lactam (n = 10) and multidrug efflux (n = 54). It also contained eight prophages, 17 other phage-related CDSs and 26 CDSs for transposases.

Conclusions

The L. hongkongensis genome possessed genes for acid and bile resistance, intestinal mucosa colonization, evasion of host defense and cytotoxicity and invasion. A broad variety of antibiotic resistance or multidrug resistance genes, a high number of prophages, other phage-related CDSs and CDSs for transposases, were also identified.     

Predicting spatial patterns of eagle migration using a mesoscale atmospheric model: a case study associated with a mountain-ridge wind development

High resolution numerical atmospheric modeling around a mountain ridge in Northeastern British Columbia (BC), Canada was performed in order to examine the influence of meteorology and topography on Golden Eagle migration pathways at the meso-scale (tens of km). During three eagle fall migration periods (2007–2009), local meteorological conditions on the day of peak bird counts were modeled using the Regional Atmospheric Modeling System (RAMS) mesoscale model. Hourly local surface wind speed, wind direction, temperature, pressure and relative humidity were also monitored during these migration periods. Eagle migration flight paths were observed from the ground and converted to three-dimensional tracks using ArcGIS. The observed eagle migration flight paths were compared with the modeled vertical velocity wind fields. Flight tracks across the study area were also simulated using the modeled vertical velocity field in a migration model based on a fluid-flow analogy. It was found that both the large-scale weather conditions and the horizontal wind fields across the study area were broadly similar on each of the modeled migration days. Nonetheless, the location and density of flight tracks across the domain varied between days, with the 2007 event producing more tracks to the southwest of the observation location than the other 2 days. The modeled wind fields suggest that it is not possible for the eagles to traverse the study area without leaving updraft regions, but birds do converge on the locations of updrafts as they move through the area. Statistical associations between observed eagles positions and the vertical velocity field suggest that to the northwest (and to a lesser extent the southwest) of the main study ridge (Johnson col), eagles can always find updrafts but that they must pass through downdraft regions in the NE and SE as they make their way across the study area. Finally, the simulated flight tracks based on the fluid-flow model and the vertical velocity fields are in general agreement with the observed flight track patterns. Our results suggest that use of high resolution meteorological fields to locate the occurrence of updrafts in proposed ridge-line wind installations could aid in predicting, and mitigating for, convergence points in raptor migrations.     

Body slap: An innovative aggressive display by breeding male gray seals (Halichoerus grypus)

Aggression in male gray seals has been extensively studied; however it is often simplistically assumed that threat signals are mainly cephalic in nature for this species. We report on an undescribed and apparently new kind of threat signal used by male gray seals we term a Body Slap. The behavior has been observed at breeding sites in eastern England since 1993 but has not been studied ethologically or reported elsewhere. The aims of this study were to describe the behavior, test the influence of topographic variation on its frequency of occurrence, examine if it is used to signal dominance or submission, and to place it in intra‐ and interspecific contexts. Our results show Body Slaps were performed in 66.3% of interactions and by 57.2% of males; it was not performed by females. The Body Slap was positively associated with the Approach and Open‐Mouth Threat behaviors but was not related to dominance; nevertheless, display rates were greater for subsequent winners. These findings suggest that the Body Slap carries information about male resource holding potential and does not signal submission. This study furthers our understanding of geographic variants of male threat behaviors and of pinniped nonvocal communication.     

Prevalence of risk factors for cardiovascular disease in Canadians 55 to 74 years of age: results from the Canadian Heart Health Surveys, 1986-1992

BACKGROUND: By 2016, the proportion of Canadians older than 65 years of age will increase to 16%, and there will be an increase in the absolute number of cases of cardiovascular disease in older Canadians. The Canadian Heart Health Surveys database provides information about this population upon which health policy related to cardiovascular disease can be based. This paper presents for the first time population-based data on the risk factors for cardiovascular disease in older Canadians. METHODS: Canadians from all 10 provinces participated in surveys of cardiovascular risk factors; health insurance registries were used as sampling frames. In each province, probability samples of 2200 adults 18 to 74 years old not living in institutions, on reserves or in military camps were asked to participate in interviews and to undergo testing at clinics for major risk factors for cardiovascular disease. RESULTS: A total of 2739 men (response rate 70%) and 2617 women (response rate 66%) aged 55 to 74 years participated in the survey and also provided follow-up clinical measurements at the clinic. Overall, 52% of participants were hypertensive, 26% had isolated systolic hypertension, and 30% had a total blood cholesterol level of 6.2 mmol/L or greater. Rates of current smoking were lower in women than men (17% v. 22%). Overall, 87% of men and 78% of women who were current smokers smoked at least 10 cigarettes per day. Only slightly more than half of participants exercised at least once a week for at least 15 minutes, and almost half had a body mass index of 27 or greater. In only 4% was no major risk factor for cardiovascular disease detected. INTERPRETATION: Significant numbers of older Canadians have one or more major risk factors for cardiovascular disease. Many of these risk factors are amenable to modification.     

Aerial photogrammetry and tag-derived tissue density reveal patterns of lipid-store body condition of humpback whales on their feeding grounds

Monitoring the body condition of free-ranging marine mammals at different life-history stages is essential to understand their ecology as they must accumulate sufficient energy reserves for survival and reproduction. However, assessing body condition in free-ranging marine mammals is challenging. We cross-validated two independent approaches to estimate the body condition of humpback whales (Megaptera novaeangliae) at two feeding grounds in Canada and Norway: animal-borne tags (n = 59) and aerial photogrammetry (n = 55). Whales that had a large length-standardized projected area in overhead images (i.e. whales looked fatter) had lower estimated tissue body density (TBD) (greater lipid stores) from tag data. Linking both measurements in a Bayesian hierarchical model to estimate the true underlying (hidden) tissue body density (uTBD), we found uTBD was lower (−3.5 kg m⁻³) in pregnant females compared to adult males and resting females, while in lactating females it was higher (+6.0 kg m⁻³). Whales were more negatively buoyant (+5.0 kg m⁻³) in Norway than Canada during the early feeding season, possibly owing to a longer migration from breeding areas. While uTBD decreased over the feeding season across life-history traits, whale tissues remained negatively buoyant (1035.3 ± 3.8 kg m⁻³) in the late feeding season. This study adds confidence to the effectiveness of these independent methods to estimate the body condition of free-ranging whales.     

Melatonin suppresses AOM/DSS-induced large bowel oncogenesis in rats

The inhibitory effects of exogenous melatonin (MEL) on colon oncogenesis were investigated using an azoxymethane (AOM)/dextran sodium sulfate (DSS) rat model. Male F344 rats initiated with a single intraperitoneal injection of AOM (20 mg/kg bw) were promoted by 1% (w/v) DSS in drinking water for 7 days. They were then given 0.4, 2 or 10 ppm MEL in drinking water for 17 weeks. At week 20, the development of colonic adenocarcinoma was significantly inhibited by the administration with MEL dose-dependently. MEL exposure modulated the mitotic and apoptotic indices in the colonic adenocarcinomas that developed and lowered the immunohistochemical expression of nuclear factor kappa B, tumor necrosis factor α, interleukin-1β and STAT3 in the epithelial malignancies. These results may indicate the beneficial effects of MEL on colitis-related colon carcinogenesis and a potential application for inhibiting colorectal cancer development in the inflamed colon.     

Molecular Analysis of H7 Avian Influenza Viruses from Australia and New Zealand: Genetic Diversity and Relationships from 1976 to 2007

Full-genome sequencing of 11 Australian and 1 New Zealand avian influenza A virus isolate (all subtype H7) has enabled comparison of the sequences of each of the genome segments to those of other subtype H7 avian influenza A viruses. The inference of phylogenetic relationships for each segment has been used to develop a model of the natural history of these viruses in Australia. Phylogenetic analysis of the hemagglutinin segment indicates that the Australian H7 isolates form a monophyletic clade. This pattern is consistent with the long-term, independent evolution that is, in this instance, associated with geographic regions. On the basis of the analysis of the other H7 hemagglutinin sequences, three other geographic regions for which similar monophyletic clades have been observed were confirmed. These regions are Eurasia plus Africa, North America, and South America. Analysis of the neuraminidase sequences from the H7N1, H7N3, and H7N7 genomes revealed the same region-based relationships. This pattern of independent evolution of Australian isolates is supported by the results of analysis of each of the six remaining genomic segments. These results, in conjunction with the occurrence of five different combinations of neuraminidase subtypes (H7N2, H7N3, H7N4, H7N6, H7N7) among the 11 Australian isolates, suggest that the maintenance host(s) is nearly exclusively associated with Australia. The single lineage of Australian H7 hemagglutinin sequences, despite the occurrence of multiple neuraminidase types, suggests the existence of a genetic pool from which a variety of reassortants arise rather than the presence of a small number of stable viral clones. This pattern of evolution is likely to occur in each of the regions mentioned above.The emergence of highly pathogenic avian influenza viruses of subtype H5N1 as a potential human pandemic disease threat has focused attention on the roles that wild birds play in the maintenance and distribution of avian influenza viruses (18, 22). Moreover, the H5 and H7 subtypes of avian influenza A virus are major causes of economic loss in poultry production through disease. In Australia, there have been five documented outbreaks of H7 subtype avian influenza A virus disease, with evidence of adaptation to the poultry host being provided by sequence data supporting the presence of high-pathogenicity avian influenza virus (HPAI) isolates in poultry. Waterfowl (Anseriformes order, particularly ducks, geese, and swans) and the waders and gulls (Charadriiformes order, particularly gulls, terns, and waders) have been found to be the major global natural reservoirs of influenza A viruses. Transmission of avian influenza viruses from wild birds to production poultry and geographic spread are dependent upon the migratory behavior of the wild bird reservoir hosts. Members of the Anseriformes and Charadriiformes orders undertake both irregular and regular transcontinental and intercontinental migrations. During these migrations, large numbers of birds congregate at aquatic feeding locations, providing ideal sites for cross-species transmission of avian influenza viruses. A variety of mechanisms have been observed whereby influenza A viruses adapt rapidly. These include genetic shifts facilitated through genome segment reassortment, as well as genetic drift through the insertion, deletion, and substitution of nucleotides. The error-prone RNA replication and a lack of error correction are the causes of drift. In vivo, this results in viral genetic diversity within any viral sample, or a quasispecies, thus providing a pool of closely related variant viruses from enabling events, such as viral adaptation to new hosts (25). Long-term sampling of water birds in North America and Europe has started to elucidate the ecology and biology of the avian influenza A virus types in the natural reservoirs in these regions (8, 18, 22). There is a suggestion that two superfamilies, the Eurasia (which in the context of this paper includes Europe, Asia, and Africa) and the Americas superfamilies, exist; however, the extent of overlap and the rate of transfer of influenza viruses between these two regions are not well-defined. Recent studies suggest that intercontinental virus exchange is slow and limited (17), while a detailed analysis of the differences between H7 hemagglutinin (HA) segments circulating in Europe and China showed that the H7 hemagglutinin segments shared a recent common ancestor and limited sequence divergence on a background of multiple reassortant virus genotypes between 1999 and 2005 (7).Avian influenza A viruses of the Oceania region (Australia, New Zealand, and southwest Pacific) have been far less well studied (3). Australia and New Zealand are at the southern extremity of a number of major bird migration pathways. Waders in the Charadriidae family migrate to south and southeastern Australia and New Zealand from their summer breeding grounds in Arctic regions of Siberia and Alaska, where they freely mix with the same or other species which migrate into the shared breeding grounds of Eurasia and the Americas (30). Pelagic seabirds of the Procellariformes order breed on and around Australian and New Zealand coasts during the southern hemisphere summer and migrate to maritime regions of the northern Pacific associated with Japan, Russia, and Alaska. Some move as far as the west coasts of North and South America (28). Unlike North and South America and Europe, where regular migrations of ducks, geese, swans, etc., are established, the members of the Anatidae family (ducks, etc.) in Australia and New Zealand are mainly endemic residents (30). However, within Australia, ducks undertake long-distance movements in response to water availability. Movements of waterfowl from northern Australia to nearby areas of Southeast Asia are believed to occur but are limited, as suggested by Wallace''s Line (19). Generally, these waterfowl movements have not been well studied (30). The risks to Australian poultry production systems by movement of H5N1 via migratory shorebirds and nomadic wildfowl have been assessed to be low using risk-based analysis techniques (9, 10).Regular and extensive surveillance sampling of migratory birds has been undertaken in North America and northern Europe (17, 18). The findings have shed significant insights into the ecology of the viruses and their hosts (8, 17). In contrast, surveillance sampling of wild birds in Asia and Oceania has been spasmodic and sparse, until the recent emergence of H5N1 highly pathogenic avian influenza virus as a poultry and human disease threat. Spasmodic and small-scale outbreaks of highly pathogenic avian influenza virus have occurred in Australian poultry production flocks located in the southeastern region of the continent. These poultry production areas are concentrated close to large human population centers (26, 33, 34). Each of the Australian outbreaks has been rapidly controlled by slaughter of infected flocks. All have been caused by avian influenza viruses of the H7 subtype, which appear to have entered production poultry from water birds, possibly wild ducks, via contaminated water supplies used on the poultry farms. Disease has occurred on five occasions: 1976 (H7N7), 1985 (H7N7), 1992 (H7N3), 1994 (H7N3), and 1997 (H7N4) (13, 14, 26, 27, 31, 34). National on-farm biosecurity measures have been focused on reducing the likelihood of future outbreaks. The availability of avian influenza virus isolates from poultry and wild birds associated with these outbreaks, along with a small number of subtype H7 avian influenza viruses isolated from wild ducks during recent national surveillance programs in Australia and New Zealand, provided the opportunity to explore the relationships of Australian and New Zealand subtype H7 avian influenza virus isolates with viruses circulating elsewhere in the world.     

Patterns of parental relatedness and pup survival in the grey seal (Halichoerus grypus)

Levels of parental relatedness can affect offspring survival and susceptibility to disease. We investigated parental relatedness of live and dead Halichoerus grypus pups between and within island populations and between possible causes of mortality. Nine microsatellites were used to calculate internal relatedness (IR) and standardized mean d2. We find that pups with higher than average levels of IR have significantly lower survival and that this varied between island populations and that certain loci contributed to the effect more than others. Although, there were no significant differences between causes of mortality, peritonitis, infection and stillborn had the highest levels of IR. These results provide evidence that parental relatedness is an important determinant of pre-weaning pup survival in the grey seal and that this may vary with cause of mortality given a larger sample size.     

Climate factors influencing bacterial count in background air samples

Total (as opposed to culturable) bacterial number counts are reported for four sites in the United Kingdom measured during campaigns over four separate seasons. These are interpreted in relation to simple climatic factors, i.e. temperature, wind speed and wind direction. Temperature has a marked effect at all four sites with data for a rural coastal site conforming best to a simple exponential model. Data for the other rural and urban locations show a baseline similar to that determined at the coastal rural location, but with some very significant positive excursions. The temperature dependence of bacterial number is found to conform to that typical of bacterial growth rates. At the coastal rural location, bacterial numbers normalised for temperature show no dependence on wind speed whilst at the inland sites there is a decrease with increasing wind speed of the form expected for a large area source. Only one site appeared to show a systematic relationship of bacterial concentrations to wind direction that being a site in the suburbs of Birmingham with highest number concentrations observed on a wind sector approaching from the city centre. PCR techniques have been used to identify predominant types of bacteria and results are presented which show that Bacillus was the dominant genus observed at the three inland sites during the winter and summer seasons. Pseudomonas appeared with comparable frequency at certain sites and seasons. There was in general a greater diversity of bacteria at the coastal site than at the inland sites.