Defining bacterial species in the genomic era : insights from the genus Acinetobacter

Background: Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data. Results: In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species. Conclusion: We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin’s vision of classification becoming, as far as is possible, genealogical

Reforming primary health care: is New Zealand's primary health care strategy achieving its early goals?

BACKGROUND: In 2001, the New Zealand government introduced its Primary Health Care Strategy (PHCS), aimed at strengthening the role of primary health care, in order to improve health and to reduce inequalities in health. As part of the Strategy, new funding was provided to reduce the fees that patients pay when they use primary health care services in New Zealand, to improve access to services and to increase service use. In this article, we estimate the impact of the new funding on general practitioner and practice nurse visit fees paid by patients and on consultation rates. The analyses involved before-and-after monitoring of fees and consultation rates in a random sample of 99 general practices and covered the period from June 2001 (pre-Strategy) to mid-2005. RESULTS: Fees fell particularly in Access (higher need, higher per capita funded) practices over time for doctor and nurse visits. Fees increased over time for many in Interim (lower need, lower per capita funded) practices, but they fell for patients aged 65 years and over as new funding was provided for this age group. There were increases in consultation rates across almost all age, funding model (Access or Interim), socio-demographic and ethnic groups. Increases were particularly high in Access practices. CONCLUSION: The Strategy has resulted in lower fees for primary health care for many New Zealanders, and consultation rates have also increased over the past few years. However, fees have not fallen by as much as expected in government policy given the amount of extra public money spent since there are limited requirements for practices to reduce patients' fees in line with increases in public funding for primary care

Motivators of couple HIV counseling and testing (CHCT) uptake in a rural setting in Uganda

Interview guide for Individuals in couple relationships (DOC 43 kb

Critical success factors for implementing risk management systems in developing countries

A review of published studies on risk management in developing countries reveals that critical success factors for implementing risk management has remained an under-researched area of investigation. This paper is aimed at investigating the perceptions of construction professionals concerning the critical success factors (CSFs) for implementation of risk management systems (IRMS). Survey data was collected from 87 construction professionals from the Iranian construction industry as a developing country. The results indicate that four factors are regarded as highly critical: ‘support from managers’, ‘inclusion of risk management in construction education and training courses for construction practitioners’, ‘attempting to deliver projects systematically’, and ‘awareness and knowledge of the process for implementing risk management’. Assessing the associations among CSFs also highlighted the crucial role of enhancing the effectiveness of knowledge management practices in construction organisations. Study also revealed that parties involved in projects do not agree on the level of importance of CSFs for implementing risk management in developing countries. This study contributes to practice and research in several ways. For practice, it increases understanding of how closely knowledge management is associated with the implementation of risk management systems in developing countries. For research, the findings would encourage construction practitioners to support effective knowledge management as a precursor to higher levels of risk management implementation on construction projects

Clonal expansion within pneumococcal serotype 6C after use of seven-valent vaccine

Streptococcus pneumoniae causes invasive infections, primarily at the extremes of life. A seven-valent conjugate vaccine (PCV7) is used to protect against invasive pneumococcal disease in children. Within three years of PCV7 introduction, we observed a fourfold increase in serotype 6C carriage, predominantly due to a single clone. We determined the whole-genome sequences of nineteen S. pneumoniae serotype 6C isolates, from both carriage (n = 15) and disease (n = 4) states, to investigate the emergence of serotype 6C in our population, focusing on a single multi-locus sequence type (MLST) clonal complex 395 (CC395). A phylogenetic network was constructed to identify different lineages, followed by analysis of variability in gene sets and sequences. Serotype 6C isolates from this single geographical site fell into four broad phylogenetically distinct lineages. Variation was seen in the 6C capsular locus and in sequences of genes encoding surface proteins. The largest clonal complex was characterised by the presence of lantibiotic synthesis locus. In our population, the 6C capsular locus has been introduced into multiple lineages by independent capsular switching events. However, rapid clonal expansion has occurred within a single MLST clonal complex. Worryingly, plasticity exists within current and potential vaccine-associated loci, a consideration for future vaccine use, target selection and design

Racial Disparities in Access to Community Water Supply Service in Wake County, North Carolina

Anecdotal evidence suggests that historically African American communities on the fringes of cities and towns in North Carolina have been systematically denied access to municipal drinking water service. This paper presents the first statistical analysis of the role of race in determining water access in these fringe areas, known as extraterritorial jurisdictions. Using publicly available property tax data, we quantified the percentage of residences with municipal water service in each census block in Wake County (the second-largest by population in North Carolina). Using the resulting water service maps plus 2010 U.S. Census data, we employed a logistic regression to assess whether race is a significant predictor of water service access in census blocks within extraterritorial jurisdictions when controlling for property value and population density. We find that every 10% increase in the African American population proportion within a census block increases the odds of exclusion from municipal water service by 3.8% (p\u3c0.05). These results suggest the need for follow-up research to explore the resulting health implications, especially because previous studies have shown that the private wells upon which such communities rely for potable water are at elevated risk of contamination from leaking septic tanks and other sources

Targeted mutagenesis in a human-parasitic nematode.

Parasitic nematodes infect over 1 billion people worldwide and cause some of the most common neglected tropical diseases. Despite their prevalence, our understanding of the biology of parasitic nematodes has been limited by the lack of tools for genetic intervention. In particular, it has not yet been possible to generate targeted gene disruptions and mutant phenotypes in any parasitic nematode. Here, we report the development of a method for introducing CRISPR-Cas9-mediated gene disruptions in the human-parasitic threadworm Strongyloides stercoralis. We disrupted the S. stercoralis twitchin gene unc-22, resulting in nematodes with severe motility defects. Ss-unc-22 mutations were resolved by homology-directed repair when a repair template was provided. Omission of a repair template resulted in deletions at the target locus. Ss-unc-22 mutations were heritable; we passed Ss-unc-22 mutants through a host and successfully recovered mutant progeny. Using a similar approach, we also disrupted the unc-22 gene of the rat-parasitic nematode Strongyloides ratti. Our results demonstrate the applicability of CRISPR-Cas9 to parasitic nematodes, and thereby enable future studies of gene function in these medically relevant but previously genetically intractable parasites

Neural Correlates of Temporal Credit Assignment in the Parietal Lobe

Empirical studies of decision making have typically assumed that value learning is governed by time, such that a reward prediction error arising at a specific time triggers temporally-discounted learning for all preceding actions. However, in natural behavior, goals must be acquired through multiple actions, and each action can have different significance for the final outcome. As is recognized in computational research, carrying out multi-step actions requires the use of credit assignment mechanisms that focus learning on specific steps, but little is known about the neural correlates of these mechanisms. To investigate this question we recorded neurons in the monkey lateral intraparietal area (LIP) during a serial decision task where two consecutive eye movement decisions led to a final reward. The underlying decision trees were structured such that the two decisions had different relationships with the final reward, and the optimal strategy was to learn based on the final reward at one of the steps (the “F” step) but ignore changes in this reward at the remaining step (the “I” step). In two distinct contexts, the F step was either the first or the second in the sequence, controlling for effects of temporal discounting. We show that LIP neurons had the strongest value learning and strongest post-decision responses during the transition after the F step regardless of the serial position of this step. Thus, the neurons encode correlates of temporal credit assignment mechanisms that allocate learning to specific steps independently of temporal discounting

THE EFFECT OF BIOMECHANICALLY FOCUSED INJURY PREVENTION TRAINING ON REDUCING ANTERIOR CRUCIATE LIGAMENT INJURY RISK AMONG FEMALE COMMUNITY LEVEL ATHLETES

This study investigated changes in biomechanical risk factors following a 9-week body-weight based training intervention focused on the dynamic control of the hip/trunk. Peak knee moments and lower limb muscle activation of female community level athletes (n=18), split into intervention (n=8) and comparison (n=10) groups, were measured during unplanned sidestepping pre/post training. Following the 9-week intervention, total muscle activation of the muscles crossing the knee decreased, which was accompanied by elevated peak knee valgus and internal rotation moments among the comparison group. Increases in peak knee valgus and internal rotation moments were not observed among the training intervention group. In the context of ACL injury risk, these findings suggest that participation in biomechanically focused training may mitigate the potentially deleterious effects of regular community level sport participation