Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study

A simple, fast, and biologically-inspired computational approach to infer genome-scale rearrangement phylogeny and ancestral gene order has been developed and applied to eight Drosophila genomes, providing insights into evolutionary chromosomal dynamics

General practitioner and the control of sexually transmissible infections

Sexually transmissible infections (STIs), one of the major preventable health problems affecting the Australian population, are often asymptomatic and, if undetected, can cause sub-fertility, infertility and chronic morbidity. In addition to these significant and costly consequences, STIs increase the risk of transmission of HIV. Given that 80% of Australian patients attend their General Practitioner (GP) each year, GPs are well placed to have a significant impact on STI transmission by diagnosing and treating both asymptomatic and symptomatic disease. Good professional practice would suggest that all GPs will undertake certain actions when they are consulted by a patient who either has symptoms of an STI or who appears to be at risk of acquiring an STI. This expectation is based on the premise that all GPs share the same detailed knowledge of STI risk factors and symptoms. It assumes that they will have no difficulty in eliciting such information from the patient, that the patient will comply with STI testing and treatment and that the patient will return for follow-up, to ensure that they and their sexual partners have been adequately treated. Given the constraints of the real world in which general practice exists, the sensitive nature of sexual health, and the stigma associated with STIs, there are many barriers to achieving such an outcome. My own previous research has highlighted some of the difficulties experienced by GPs in the area of STI control. This study has used data from four different sources (policy and stakeholder documents, literature, key informant interviews and my own past research) to examine ideal practice and actual practice in the prevention and treatment of STIs. A number of discrepancies were identified, and from these arose a series of recommendations for ways of making STI control in general practice less complex. To ensure that the results of the study were firmly embedded in the reality of general practice, comments on the recommendations were sought from GPs employed in a variety of practice settings, including those with low STI caseloads. These comments were used to modify the recommendations to ensure they would offer a practical and effective contribution to STI control in Victoria

Phylogenetic Relationship of the Complete Rauscher Murine Leukemia Virus Genome with Other Murine Leukemia Virus Genomes

AbstractWe report the complete nucleotide sequence of the genome of Rauscher murine leukemia virus (R-MuLV), the replication-competent helper virus present in the Rauscher virus complex, and its phylogenetic relationship with other murine leukemia virus genomes. An overall sequence identity of 97.6% was found between R-MuLV and the Friend helper virus (F-MuLV), and the two viruses were closely related on the phylogenetic trees constructed from eithergag, pol,orenvsequences. Moloney murine leukemia virus (Mo-MuLV) was the next closest relative to R-MuLV and F-MuLV on all trees, followed by Akv and radiation leukemia virus (RadLV). The most distantly related helper virus was Hortulanus murine leukemia virus (Ho-MuLV). Interestingly, Cas-Br-E branched with Mo-MuLV on thegagandpoltrees, whereas on theenvtree, it revealed the highest degree of relatedness to Ho-MuLV, possibly due to an ancient recombination with an Ho-MuLV ancestor. In summary, a phylogenetic analysis involving various MuLVs has been performed, in which the postulated close relationship between R-MuLV and F-MuLV has been confirmed, consistent with the pathobiology of the two viruses

Telling partners about chlamydia: how acceptable are the new technologies?

BACKGROUND Partner notification is accepted as a vital component in the control of chlamydia. However, in reality, many sexual partners of individuals diagnosed with chlamydia are never informed of their risk. The newer technologies of email and SMS have been used as a means of improving partner notification rates. This study explored the use and acceptability of different partner notification methods to help inform the development of strategies and resources to increase the number of partners notified. METHODS Semi-structured telephone interviews were conducted with 40 people who were recently diagnosed with chlamydia from three sexual health centres and two general practices across three Australian jurisdictions. RESULTS Most participants chose to contact their partners either in person (56%) or by phone (44%). Only 17% chose email or SMS. Participants viewed face-to-face as the "gold standard" in partner notification because it demonstrated caring, respect and courage. Telephone contact, while considered insensitive by some, was often valued because it was quick, convenient and less confronting. Email was often seen as less personal while SMS was generally considered the least acceptable method for telling partners. There was also concern that emails and SMS could be misunderstood, not taken seriously or shown to others. Despite these, email and SMS were seen to be appropriate and useful in some circumstances. Letters, both from the patients or from their doctor, were viewed more favourably but were seldom used. CONCLUSION These findings suggest that many people diagnosed with chlamydia are reluctant to use the new technologies for partner notification, except in specific circumstances, and our efforts in developing partner notification resources may best be focused on giving patients the skills and confidence for personal interaction.The study was funded by the Australian Federal Government Department of Health and Ageing Chlamydia Pilot Program of Targeted Grants

Women’s Views and Experiences of the Triggers for Onset of Bacterial Vaginosis and Exacerbating Factors Associated with Recurrence

Background Bacterial vaginosis (BV) is the most common vaginal infection affecting women of childbearing age. While the aetiology and transmissibility of BV remain unclear, there is strong evidence to suggest an association between BV and sexual activity. This study explored women’s views and experiences of the triggers for BV onset and factors associated with recurrence. Methods A descriptive, social constructionist approach was chosen as the framework for the study. Thirty five women of varying sexual orientation who had experienced recurrent BV in the past five years took part in semi-structured interviews. Results The majority of women predominantly reported sexual contact triggered the onset of BV and sexual and non-sexual factors precipitated recurrence. Recurrence was most commonly referred to in terms of a ‘flare-up’ of symptoms. The majority of women did not think BV was a sexually transmitted infection however many reported being informed this by their clinician. Single women who attributed BV onset to sex with casual partners were most likely to display self-blame tendencies and to consider changing their future sexual behaviour. Women who have sex with women (WSW) were more inclined to believe their partner was responsible for the transmission of or reinfection with BV and seek partner treatment or change their sexual practices. Conclusion Findings from this study strongly suggest women believe that BV onset is associated with sexual activity, concurring with epidemiological data which increasingly suggest BV may be sexually transmitted. Exacerbating factors associated with recurrence were largely heterogeneous and may reflect the fact it is difficult to determine whether recurrence is due to persistent BV or a new infection in women. There was however evidence to suggest possible transmission and reinfection among WSW, reinforcing the need for new approaches to treatment and management strategies including male and female partner treatment trials.Dr. Jade Bilardi is in receipt of an NHMRC Early Career Fellowship No 1013135

Improving chlamydia knowledge should lead to increased chlamydia testing among Australian general practitioners: a cross-sectional study of chlamydia testing uptake in general practice

Female general practitioners (GPs) have higher chlamydia testing rates than male GPs, yet it is unclear whether this is due to lack of knowledge among male GPs or because female GPs consult and test more female patients

Women’s Views and Experiences of the Triggers for Onset of Bacterial Vaginosis and Exacerbating Factors Associated with Recurrence

Background Bacterial vaginosis (BV) is the most common vaginal infection affecting women of childbearing age. While the aetiology and transmissibility of BV remain unclear, there is strong evidence to suggest an association between BV and sexual activity. This study explored women’s views and experiences of the triggers for BV onset and factors associated with recurrence. Methods A descriptive, social constructionist approach was chosen as the framework for the study. Thirty five women of varying sexual orientation who had experienced recurrent BV in the past five years took part in semi-structured interviews. Results The majority of women predominantly reported sexual contact triggered the onset of BV and sexual and non-sexual factors precipitated recurrence. Recurrence was most commonly referred to in terms of a ‘flare-up’ of symptoms. The majority of women did not think BV was a sexually transmitted infection however many reported being informed this by their clinician. Single women who attributed BV onset to sex with casual partners were most likely to display self-blame tendencies and to consider changing their future sexual behaviour. Women who have sex with women (WSW) were more inclined to believe their partner was responsible for the transmission of or reinfection with BV and seek partner treatment or change their sexual practices. Conclusion Findings from this study strongly suggest women believe that BV onset is associated with sexual activity, concurring with epidemiological data which increasingly suggest BV may be sexually transmitted. Exacerbating factors associated with recurrence were largely heterogeneous and may reflect the fact it is difficult to determine whether recurrence is due to persistent BV or a new infection in women. There was however evidence to suggest possible transmission and reinfection among WSW, reinforcing the need for new approaches to treatment and management strategies including male and female partner treatment trials.Dr. Jade Bilardi is in receipt of an NHMRC Early Career Fellowship No 1013135

Women’s Management of Recurrent Bacterial Vaginosis and Experiences of Clinical Care: A Qualitative Study.

Background Few data are available on how women manage recurring bacterial vaginosis (BV) and their experiences of the clinical care of this condition. This study aimed to explore women’s recurrent BV management approaches and clinical care experiences, with a view to informing and improving the clinical management of BV. Methods A descriptive, social constructionist approach was chosen as the framework for the study. Thirty-five women of varying sexual orientation who had experienced recurrent BV in the past 5 years took part in semi-structured interviews. Results The majority of women reported frustration and dissatisfaction with current treatment regimens and low levels of satisfaction with the clinical management of BV. Overall, women disliked taking antibiotics regularly, commonly experienced adverse side effects from treatment and felt frustrated at having symptoms recur quite quickly after treatment. Issues in clinical care included inconsistency in advice, misdiagnosis and inappropriate diagnostic approaches and insensitive or dismissive attitudes. Women were more inclined to report positive clinical experiences with sexual health physicians than primary care providers. Women’s frustrations led most to try their own self-help remedies and lifestyle modifications in an attempt to treat symptoms and prevent recurrences, including well-known risk practices such as douching. Conclusion In the face of considerable uncertainty about the cause of BV, high rates of recurrence, unacceptable treatment options and often insensitive and inconsistent clinical management, women are trying their own self-help remedies and lifestyle modifications to prevent recurrences, often with little effect. Clinical management of BV could be improved through the use of standardised diagnostic approaches, increased sensitivity and understanding of the impact of BV, and the provision of evidence based advice about known BV related risk factors.Dr. Jade Bilardi is in receipt of a National Health and Medical Research Council Early Career Fellowship (No. 1013135)

Better than nothing? Patient-delivered partner therapy and partner notification for chlamydia: the views of Australian general practitioners

BACKGROUND Genital chlamydia is the most commonly notified sexually transmissible infection (STI) in Australia and worldwide and can have serious reproductive health outcomes. Partner notification, testing and treatment are important facets of chlamydia control. Traditional methods of partner notification are not reaching enough partners to effectively control transmission of chlamydia. Patient-delivered partner therapy (PDPT) has been shown to improve the treatment of sexual partners. In Australia, General Practitioners (GPs) are responsible for the bulk of chlamydia testing, diagnosis, treatment and follow up. This study aimed to determine the views and practices of Australian general practitioners (GPs) in relation to partner notification and PDPT for chlamydia and explored GPs' perceptions of their patients' barriers to notifying partners of a chlamydia diagnosis. METHODS In-depth, semi-structured telephone interviews were conducted with 40 general practitioners (GPs) from rural, regional and urban Australia from November 2006 to March 2007. Topics covered: GPs' current practice and views about partner notification, perceived barriers and useful supports, previous use of and views regarding PDPT.Transcripts were imported into NVivo7 and subjected to thematic analysis. Data saturation was reached after 32 interviews had been completed. RESULTS Perceived barriers to patients telling partners (patient referral) included: stigma; age and cultural background; casual or long-term relationship, ongoing relationship or not. Barriers to GPs undertaking partner notification (provider referral) included: lack of time and staff; lack of contact details; uncertainty about the legality of contacting partners and whether this constitutes breach of patient confidentiality; and feeling both personally uncomfortable and inadequately trained to contact someone who is not their patient. GPs were divided on the use of PDPT--many felt concerned that it is not best clinical practice but many also felt that it is better than nothing.GPs identified the following factors which they considered would facilitate partner notification: clear clinical guidelines; a legal framework around partner notification; a formal chlamydia screening program; financial incentives; education and practical support for health professionals, and raising awareness of chlamydia in the community, in particular amongst young people. CONCLUSIONS GPs reported some partners do not seek medical treatment even after they are notified of being a sexual contact of a patient with chlamydia. More routine use of PDPT may help address this issue however GPs in this study had negative attitudes to the use of PDPT. Appropriate guidelines and legislation may make the use of PDPT more acceptable to Australian GPs.The Australian Federal Government Department of Health and Ageing Chlamydia Pilot Program of Targeted Grants funded the study