Whole Genome Sequencing Reveals Local Transmission Patterns of Mycobacterium bovis in Sympatric Cattle and Badger Populations

Whole genome sequencing (WGS) technology holds great promise as a tool for the forensic epidemiology of bacterial pathogens. It is likely to be particularly useful for studying the transmission dynamics of an observed epidemic involving a largely unsampled 'reservoir' host, as for bovine tuberculosis (bTB) in British and Irish cattle and badgers. BTB is caused by Mycobacterium bovis, a member of the M. tuberculosis complex that also includes the aetiological agent for human TB. In this study, we identified a spatio-temporally linked group of 26 cattle and 4 badgers infected with the same Variable Number Tandem Repeat (VNTR) type of M. bovis. Single-nucleotide polymorphisms (SNPs) between sequences identified differences that were consistent with bacterial lineages being persistent on or near farms for several years, despite multiple clear whole herd tests in the interim. Comparing WGS data to mathematical models showed good correlations between genetic divergence and spatial distance, but poor correspondence to the network of cattle movements or within-herd contacts. Badger isolates showed between zero and four SNP differences from the nearest cattle isolate, providing evidence for recent transmissions between the two hosts. This is the first direct genetic evidence of M. bovis persistence on farms over multiple outbreaks with a continued, ongoing interaction with local badgers. However, despite unprecedented resolution, directionality of transmission cannot be inferred at this stage. Despite the often notoriously long timescales between time of infection and time of sampling for TB, our results suggest that WGS data alone can provide insights into TB epidemiology even where detailed contact data are not available, and that more extensive sampling and analysis will allow for quantification of the extent and direction of transmission between cattle and badgers. © 2012 Biek et al.

Forecasting invasions: resource use by mussels informs invasion patterns along the South African coast

Invasive species are often more able to rapidly and efficiently utilise resources than natives, and comparing per capita resource use at different resource densities among invaders and trophically analogous natives could allow for reliable predictions of invasiveness. In South Africa, invasion by the Mediterranean mussel Mytilus galloprovincialis has transformed wave-exposed shores, negatively affecting native mussel species. Currently, South Africa is experiencing a second mussel invasion with the recent detection of the South American Semimytilus algosus. We tested per capita uptake of an algal resource by invading M. galloprovincialis, S. algosus, and the native Aulacomya atra at different algal concentrations and temperatures, representing the west and south coasts of South Africa, to examine whether their per capita resource use could be a predictor of their spread and subsequent invasiveness. Regardless of temperature, M. galloprovincialis was the most efficient consumer, significantly reducing algal cells compared to the other species when the resource was presented in both low and high starting densities. Furthermore, these findings aligned with a greater biomass of M. galloprovincialis on the shore in comparison with the other species. Resource use by the new invader S. algosus was dependent on the density of resource and, although this species was efficient at low algal concentrations at cooler temperatures, this pattern broke down at higher algal densities. This was once more reflected in lower biomass in surveys of this species along the cool west coast. We therefore forecast that S. algosus will be become established along the south coast; however, we also predict that M. galloprovincialis will maintain dominance on these shores.

Exploiting Human Resource Requirements to Infer Human Movement Patterns for Use in Modelling Disease Transmission Systems: An Example from Eastern Province, Zambia

In this research, an agent-based model (ABM) was developed to generate human movement routes between homes and water resources in a rural setting, given commonly available geospatial datasets on population distribution, land cover and landscape resources. ABMs are an object-oriented computational approach to modelling a system, focusing on the interactions of autonomous agents, and aiming to assess the impact of these agents and their interactions on the system as a whole. An A* pathfinding algorithm was implemented to produce walking routes, given data on the terrain in the area. A* is an extension of Dijkstra's algorithm with an enhanced time performance through the use of heuristics. In this example, it was possible to impute daily activity movement patterns to the water resource for all villages in a 75 km long study transect across the Luangwa Valley, Zambia, and the simulated human movements were statistically similar to empirical observations on travel times to the water resource (Chi-squared, 95% confidence interval). This indicates that it is possible to produce realistic data regarding human movements without costly measurement as is commonly achieved, for example, through GPS, or retrospective or real-time diaries. The approach is transferable between different geographical locations, and the product can be useful in providing an insight into human movement patterns, and therefore has use in many human exposure-related applications, specifically epidemiological research in rural areas, where spatial heterogeneity in the disease landscape, and space-time proximity of individuals, can play a crucial role in disease spread.

Starting slow: the effects of response-switching frequency on patterns of cardiovascular reactivity

Research findings suggest that switching between competing response sets can be resource demanding. The current study focused on concurrent health-relevant physiological effects of task switching by assessing cardiovascular response at varying levels of switch frequency. The participants performed a response-switching task at three different levels of response set switching frequency (low, medium and high) while measurements of blood pressure and heart rate were taken. One group was exposed to response-switching frequency conditions in the order low → medium → high, while the other group was exposed to the same task conditions in the reverse order (i.e. high → medium → low). The results showed that the participants in the low → medium → high switch frequency group recovered faster from initially heightened systolic blood pressure when compared with participants in the high → medium → low group. It is concluded that the results point to a physiological "carry over" effect associated with beginning a task at rapid response switching frequency levels, and suggest the importance of habituation to task demands as a means of offsetting potentially unhealthy levels of reactivity. Implications for modern work environments are discussed.

Patterns of co‑occurrence and interactions between age classes of the common triplefin, Forsterygion lapillum

Many marine organisms have pelagic larval stages that settle into benthic habitats occupied by older individuals; however, a mechanistic understanding of inter cohort interactions remains elusive for most species. Patterns of spatial covariation in the densities of juvenile and adult age classes of a small temperate reef fish, the common triplefin (Forsterygion lapillum), were evaluated during the recruitment season (Feb–Mar, 2011) in Wellington, New Zealand (41°17′S, 174°46′E). The relationship between juvenile and adult density among sites was best approximated by a dome-shaped curve, with a negative correlation between densities of juveniles and adults at higher adult densities. The curve shape was temporally variable, but was unaffected by settlement habitat type (algal species). A laboratory experiment using a “multiple-predator effects”design tested the hypothesis that increased settler mortality in the presence of adults (via enhanced predation risk or cannibalism) contributed to the observed negative relationship between juveniles and adults. Settler mortality did not differ between controls and treatments that contained either one (p = 0.08) or two (p = 0.09) adults. However, post hoca analyses revealed a significant positive correlation between the mean length of juveniles used in experimental trials and survival of juveniles in these treatments, suggesting that smaller juveniles may be vulnerable to cannibalism. There was no evidence for risk enhancement or predator interference when adults were present alongside a hetero specific predator (F. varium). These results highlight the complex nature of intercohort relationships in shaping recruitment patterns and add to the growing body of literature recognizing the importance of age class interactions.

Between-taxon matching of common and rare species richness patterns

Aim: Our primary aim is to understand how assemblages of rare (restricted range) and common (widespread) species are correlated with each other among different taxa. We tested the proposition that marine species richness patterns of rare and common species differ, both within a taxon in their contribution to the richness pattern of the full assemblage and among taxa in the strength of their correlations with each other. Location The UK intertidal zone. Methods: We used high-resolution marine datasets for UK intertidal macroalgae, molluscs and crustaceans each with more than 400 species. We estimated the relative contribution of rare and common species, treating rarity and commonness as a continuous spectrum, to spatial patterns in richness using spatial crosscorrelations. Correlation strength and significance was estimated both within and between taxa. Results: Common species drove richness patterns within taxa, but rare species contributed more when species were placed on an equal footing via scaling by binomial variance. Between taxa, relatively small sub-assemblages (fewer than 60 species) of common species produced the maximum correlation with each other, regardless of taxon pairing. Cross-correlations between rare species were generally weak, with maximum correlation occurring between small sub-assemblages in only one case. Cross-correlations between common and rare species of different taxa were consistently weak or absent. Main conclusions: Common species in the three marine assemblages were congruent in their richness patterns, but rare species were generally not. The contrast between the stronger correlations among common species and the weak or absent correlations among rare species indicates a decoupling of the processes driving common and rare species richness patterns. The internal structure of richness patterns of these marine taxa is similar to that observed for terrestrial taxa.

Epidemiology, Patterns of Care, and Mortality for Patients With Acute Respiratory Distress Syndrome in Intensive Care Units in 50 Countries

Importance Limited information exists about the epidemiology, recognition, management, and outcomes of patients with the acute respiratory distress syndrome (ARDS).

Objectives To evaluate intensive care unit (ICU) incidence and outcome of ARDS and to assess clinician recognition, ventilation management, and use of adjuncts—for example prone positioning—in routine clinical practice for patients fulfilling the ARDS Berlin Definition.

Design, Setting, and Participants The Large Observational Study to Understand the Global Impact of Severe Acute Respiratory Failure (LUNG SAFE) was an international, multicenter, prospective cohort study of patients undergoing invasive or noninvasive ventilation, conducted during 4 consecutive weeks in the winter of 2014 in a convenience sample of 459 ICUs from 50 countries across 5 continents.

Exposures Acute respiratory distress syndrome.

Main Outcomes and Measures The primary outcome was ICU incidence of ARDS. Secondary outcomes included assessment of clinician recognition of ARDS, the application of ventilatory management, the use of adjunctive interventions in routine clinical practice, and clinical outcomes from ARDS.

Results Of 29 144 patients admitted to participating ICUs, 3022 (10.4%) fulfilled ARDS criteria. Of these, 2377 patients developed ARDS in the first 48 hours and whose respiratory failure was managed with invasive mechanical ventilation. The period prevalence of mild ARDS was 30.0% (95% CI, 28.2%-31.9%); of moderate ARDS, 46.6% (95% CI, 44.5%-48.6%); and of severe ARDS, 23.4% (95% CI, 21.7%-25.2%). ARDS represented 0.42 cases per ICU bed over 4 weeks and represented 10.4% (95% CI, 10.0%-10.7%) of ICU admissions and 23.4% of patients requiring mechanical ventilation. Clinical recognition of ARDS ranged from 51.3% (95% CI, 47.5%-55.0%) in mild to 78.5% (95% CI, 74.8%-81.8%) in severe ARDS. Less than two-thirds of patients with ARDS received a tidal volume 8 of mL/kg or less of predicted body weight. Plateau pressure was measured in 40.1% (95% CI, 38.2-42.1), whereas 82.6% (95% CI, 81.0%-84.1%) received a positive end-expository pressure (PEEP) of less than 12 cm H2O. Prone positioning was used in 16.3% (95% CI, 13.7%-19.2%) of patients with severe ARDS. Clinician recognition of ARDS was associated with higher PEEP, greater use of neuromuscular blockade, and prone positioning. Hospital mortality was 34.9% (95% CI, 31.4%-38.5%) for those with mild, 40.3% (95% CI, 37.4%-43.3%) for those with moderate, and 46.1% (95% CI, 41.9%-50.4%) for those with severe ARDS.

Conclusions and Relevance Among ICUs in 50 countries, the period prevalence of ARDS was 10.4% of ICU admissions. This syndrome appeared to be underrecognized and undertreated and associated with a high mortality rate. These findings indicate the potential for improvement in the management of patients with ARDS.

Sexual Abuse in Malawi: Patterns of Disclosure

Potential human immunodeficiency virus transmission makes prompt disclosure of child sexual abuse in Africa critical. The pattern of disclosure of 133 children presenting to the largest hospital in Malawi were analyzed. Eighty percent presented early enough for effective use of HIV postexposure prophylaxis. Seventy-five percent of children made a disclosure of child sexual abuse; 29% spontaneously and 47% after prompting. Disclosures were most commonly made to a parent, and age did not affect the pattern of disclosure. The number of children reporting child sexual abuse is increasing, possibly because of increasing awareness, availability of services, and fear of HIV. Although prompt disclosure rates were relatively high, facilitating easier disclosure of child sexual abuse by a free telephone help-line and better training of teachers may be helpful. 

Climate drives temporal replacement and nested‐resultant richness patterns of Scottish coastal vegetation

Beta diversity quantifies spatial and/or temporal variation in species composition. It is comprised of two distinct components, species replacement and nestedness, which derive from opposing ecological processes. Using Scotland as a case study and a β-diversity partitioning framework, we investigate temporal replacement and nestedness patterns of coastal grassland species over a 34-yr time period. We aim to 1) understand the influence of two potentially pivotal processes (climate and land-use changes) on landscape-scale (5 × 5 km) temporal replacement and nestedness patterns, and 2) investigate whether patterns from one β-diversity component can mask observable patterns in the other.

We summarised key aspects of climate driven macro-ecological variation as measures of variance, long-term trends, between-year similarity and extremes, for three important climatic predictors (minimum temperature, water-balance and growing degree-days). Shifts in landscape-scale heterogeneity, a proxy of land-use change, was summarised as a spatial multiple-site dissimilarity measure. Together, these climatic and spatial predictors were used in a multi-model inference framework to gauge the relative contribution of each on temporal replacement and nestedness patterns.

Temporal β-diversity patterns were reasonably well explained by climate change but weakly explained by changes in landscape-scale heterogeneity. Climate was shown to have a greater influence on temporal nestedness than replacement patterns over our study period, linking nestedness patterns, as a result of imbalanced gains and losses, to climatic warming and extremes respectively. Important climatic predictors (i.e. growing degree-days) of temporal β-diversity were also identified, and contrasting patterns between the two β-diversity components revealed.

Results suggest climate influences plant species recruitment and establishment processes of Scotland's coastal grasslands, and while species extinctions take time, they are likely to be facilitated by climatic perturbations. Our findings also highlight the importance of distinguishing between different components of β-diversity, disentangling contrasting patterns than can mask one another.

Patterns and predictors of help-seeking contacts with health services and general practitioner detection of suicidality prior to suicide: a cohort analysis of suicides occurring over a two-year period

Background: Contact with primary care and psychiatric services prior to suicide may be considerable, presenting
opportunities for intervention. However, there is scant knowledge on the frequency, nature and determinants of
contact.
Method: Retrospective cohort study-an analysis of deaths recorded as suicide by the Northern Ireland Coroner’s
Office linked with data from General Practice patient records over a 2 year period
Results: Eighty-seven per cent of suicides were in contact with General Practice services in the 12 months before
suicide. The frequency of contact with services was considerable, particularly among patients with a common
mental disorder or substance misuse problems. A diagnosis of psychiatric problems was absent in 40 % of suicides.
Excluding suicide attempts, the main predictors of a noted general practitioner concern for patient suicidality are
male gender, frequency of consultations, diagnosis of mental illness and substance misuse.
Conclusions: Despite widespread and frequent contact, a substantial proportion of suicidal people were
undiagnosed and untreated for mental health problems. General Practitioner alertness to suicidality may be too
narrowly focused.