Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex.

Models on how bacterial lineages differentiate increase our understanding of early bacterial speciation events and the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen. The emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify the phoR gene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the Mycobacterium tuberculosis complex from its ancestor. Previous evidence showed that phoR mutations played a central role in the adaptation of the pathogen to different host species. Now, we show that phoR mutations have been under selection during the early spread of human tuberculosis, during later expansions, and in ongoing transmission events. Our results show that linking pathogen evolution across evolutionary and epidemiological time scales points to past and present virulence determinants.

Collaborative Occupational Therapy: Teachers' Impressions of the Partnering for Change (P4C) Model.

AIMS: Occupational therapists (OTs) often face barriers when trying to collaborate with teachers in school-based settings. Partnering for change (P4C), a collaborative practice model designed to support children with developmental coordination disorder, could potentially support all students with special needs. Therefore, the aim of this study was to explore how teachers experience OT services delivered using the P4C model to support children with a variety of special needs. METHODS: P4C was implemented at one elementary school in Courtenay, British Columbia. Eleven teachers participated in two focus groups and a one-on-one interview to gather descriptive, qualitative data. Grounded theory techniques were used for data analysis. RESULTS: Four themes (collaborating in the thick of it all, learning and taking risks, managing limited time and resources, and appreciating responsive OT support) represented teachers' experiences of P4C. CONCLUSIONS: Teachers strongly preferred collaborative OT services based on the P4C model. Students with a variety of special needs were supported within their classrooms as teachers learned new strategies from the OT and found ways to embed these strategies into their daily routines.

Zoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans.

The emergence of Clostridium difficile as a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital-associated C. difficile RT027 lineage, the community-associated C. difficile RT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here, we applied whole-genome phylogenetic analysis of 248 C. difficile RT078 strains from 22 countries. Our results demonstrate limited geographical clustering for C. difficile RT078 and extensive coclustering of human and animal strains, thereby revealing a highly linked intercontinental transmission network between humans and animals. Comparative whole-genome analysis reveals indistinguishable accessory genomes between human and animal strains and a variety of antimicrobial resistance genes in the pangenome of C. difficile RT078. Thus, bidirectional spread of C. difficile RT078 between farm animals and humans may represent an unappreciated route disseminating antimicrobial resistance genes between humans and animals. These results highlight the importance of the "One Health" concept to monitor infectious disease emergence and the dissemination of antimicrobial resistance genes.

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures.

BACKGROUND: Chlamydia abortus (formerly Chlamydophila abortus) is an economically important livestock pathogen, causing ovine enzootic abortion (OEA), and can also cause zoonotic infections in humans affecting pregnancy outcome. Large-scale genomic studies on other chlamydial species are giving insights into the biology of these organisms but have not yet been performed on C. abortus. Our aim was to investigate a broad collection of European isolates of C. abortus, using next generation sequencing methods, looking at diversity, geographic distribution and genome dynamics. RESULTS: Whole genome sequencing was performed on our collection of 57 C. abortus isolates originating primarily from the UK, Germany, France and Greece, but also from Tunisia, Namibia and the USA. Phylogenetic analysis of a total of 64 genomes shows a deep structural division within the C. abortus species with a major clade displaying limited diversity, in addition to a branch carrying two more distantly related Greek isolates, LLG and POS. Within the major clade, seven further phylogenetic groups can be identified, demonstrating geographical associations. The number of variable nucleotide positions across the sampled isolates is significantly lower than those published for C. trachomatis and C. psittaci. No recombination was identified within C. abortus, and no plasmid was found. Analysis of pseudogenes showed lineage specific loss of some functions, notably with several Pmp and TMH/Inc proteins predicted to be inactivated in many of the isolates studied. CONCLUSIONS: The diversity within C. abortus appears to be much lower compared to other species within the genus. There are strong geographical signatures within the phylogeny, indicating clonal expansion within areas of limited livestock transport. No recombination has been identified within this species, showing that different species of Chlamydia may demonstrate different evolutionary dynamics, and that the genome of C. abortus is highly stable.

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.

Chlamydia trachomatis clinical isolates identified as tetracycline resistant do not exhibit resistance in vitro: whole-genome sequencing reveals a mutation in porB but no evidence for tetracycline resistance genes.

Chlamydia trachomatis is the most common bacterial sexually transmitted infection worldwide and the leading cause of preventable blindness in developing countries. Tetracycline is commonly the drug of choice for treating C. trachomatis infections, but cases of antibiotic resistance in clinical isolates have previously been reported. Here, we used antibiotic resistance assays and whole-genome sequencing to interrogate the hypothesis that two clinical isolates (IU824 and IU888) have acquired mechanisms of antibiotic resistance. Immunofluorescence staining was used to identify C. trachomatis inclusions in cell cultures grown in the presence of tetracycline; however, only antibiotic-free control cultures yielded the strong fluorescence associated with the presence of chlamydial inclusions. Infectivity was lost upon passage of harvested cultures grown in the presence of tetracycline into antibiotic-free medium, so we conclude that these isolates were phenotypically sensitive to tetracycline. Comparisons of the genome and plasmid sequences for the two isolates with tetracycline-sensitive strains did not identify regions of low sequence identity that could accommodate horizontally acquired resistance genes, and the tetracycline binding region of the 16S rRNA gene was identical to that of the sensitive control strains. The porB gene of strain IU824, however, was found to contain a premature stop codon not previously identified, which is noteworthy but unlikely to be related to tetracycline resistance. In conclusion, we found no evidence of tetracycline resistance in the two strains investigated, and it seems most likely that the small, aberrant inclusions previously identified resulted from the high chlamydial load used in the original antibiotic resistance assays.

Quality of life domains affected in children with developmental coordination disorder: a systematic review.

The quality of life (QOL) of children with developmental coordination disorder (DCD) is largely unknown, but evidence suggests that multiple QOL domains are affected by the disorder. While DCD is primarily considered a motor disorder, multiple studies have reported psychological and social concerns in children with this condition. Our primary aim was to present the current state of the evidence regarding the physical, psychological, and social QOL domains that can be affected in children with DCD. Systematic review of articles from seven databases through November 2010 (MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC, CDSR, DARE) was conducted. Search terms included developmental coordination disorder, dyspraxia, quality of life, life satisfaction, well-being, activities of daily living, and participation. Two independent reviewers screened titles, abstracts, and full-text articles. Studies meeting the following criteria were selected: (1) sample comprised solely of individuals with coordination difficulties consistent with DCD; (2) outcome measures related to physical, psychological, or socials domains of QOL; and (3) articles published in English. Data were extracted by one author and verified by a second. Outcomes were categorized according to physical, psychological and social domains of QOL and study quality was rated by case definitions of DCD based on diagnostic criteria as per the Diagnostic and Statistical Manual - 4th edition. Forty-one articles were included. Most studies reported significantly poorer results in physical, psychological and social functioning in children with DCD compared with peers. Despite the impact of DCD on multiple domains, only one study used a QOL measure as an outcome. Although DCD impacts several QOL domains, the QOL of children with this disorder remains largely unknown. The next critical step is for clinicians and researchers to use QOL measures to gather information on how DCD may affect the QOL of children with this disorder.

Exercise prescription after fragility fracture in older adults: a scoping review.

The purpose of this study is to identify and chart research literature on safety, efficacy, or effectiveness of exercise prescription following fracture in older adults. We conducted a systematic, research-user-informed, scoping review. The population of interest was adults aged ≥45 years with any fracture. "Exercise prescription" included post-fracture therapeutic exercise, physical activity, or rehabilitation interventions. Eligible designs included knowledge synthesis studies, primary interventional studies, and observational studies. Trained reviewers independently evaluated citations for inclusion. A total of 9,415 citations were reviewed with 134 citations (119 unique studies) identified: 13 knowledge syntheses, 95 randomized or controlled clinical trials, and 11 "other" designs, representing 74 articles on lower extremity fractures, 34 on upper extremity, eight on vertebral, and three on mixed body region fractures. Exercise prescription characteristics were often missing or poorly described. Six general categories emerged describing exercise prescription characteristics: timing post-fracture, person prescribing, program design, functional focus, exercise script parameters, and co-interventions. Upper extremity and ankle fracture studies focused on fracture healing or structural impairment outcomes, whereas hip fracture studies focused more on activity limitation outcomes. The variety of different outcome measures used made pooling or comparison of outcomes difficult. There was insufficient information to identify evidence-informed parameters for safe and effective exercise prescription for older adults following fracture. Key gaps in the literature include limited numbers of studies on exercise prescription following vertebral fracture, poor delineation of effectiveness of different strategies for early post-fracture mobilization following upper extremity fracture, and inconsistent details of exercise prescription characteristics after lower extremity fracture.

Effects of therapeutic exercise for persons with osteoporotic vertebral fractures: a systematic review.

UNLABELLED: A systematic literature review was conducted and revealed nine studies investigating the effects of therapeutic exercise for persons with osteoporotic vertebral fractures. Although modest improvements were noted in strength and balance, results were inconsistent in supporting therapeutic exercise as effective in improving outcomes such as pain and quality of life (QOL). INTRODUCTION: The purpose of this systematic review was to investigate the effects of therapeutic exercise as an intervention for patients over age 45 years with one or more osteoporotic vertebral fractures. The effects of the intervention on the following outcomes are summarized in this review: pain/analgesic use, QOL, function, strength, balance, range of motion, bone mineral density, and incidence of future fractures. METHODS: A systematic literature review of therapeutic exercise as a treatment for persons with osteoporotic vertebral fractures was conducted. Studies were retrieved from six databases, screened for inclusion, and assessed for methodological quality. Results were analyzed qualitatively based on levels of evidence, methodological rigor, and consistency of findings across studies within each of the eight health-related outcomes. RESULTS: Due to inconsistent results across the nine studies included in the review, there is only limited or inconsistent evidence for the effectiveness of therapeutic exercise on each of the outcomes investigated. CONCLUSIONS: Due to lack of high-quality, consistent research on the effects of exercise for persons with vertebral fractures, no definitive conclusions can be drawn from this systematic review. Positive trends were identified with regard to improvements in strength and balance, with no increase in pain following exercise protocols. Future research is needed in this area.

Helpful communications during the diagnostic period: an interpretive description of patient preferences.

With a diagnosis of cancer, life changes for patients in a profound manner. The window of time known as cancer diagnosis is one of considerable turbulence and distress for patients. Therefore, diagnosis constitutes a time during which communication with healthcare professionals is of particular importance in setting the stage for the way cancer illness will be experienced. Our research explores communications throughout the cancer trajectory from the perspective of patients themselves. We are following a sample of 60 cancer patients, representing a range of tumour sites, from the early diagnostic period through to recovery, chronic, or advanced disease. Using interpretive description analysis techniques, we document patterns and themes related to various components of the cancer journey. In this paper, we focus on themes related to perceived helpful communication during the diagnosis experience as reported by our study participants both at the time of being newly diagnosed patients, and as they reflect on that period 12 months later. These findings illuminate experiential issues of importance to patients in relation to cancer care communication and the manner in which helpful communications during this sensitive time may facilitate the subsequent experience living with and obtaining care for cancer.

A sensitive HPLC-MS-MS assay for quantitative determination of midazolam in dog plasma.

The clinical pharmacokinetics of midazolam have been extensively studied, due to its high clearance by CYP3A4 and sensitivity to drug-drug interactions. In order to investigate the potential to model drug-drug interactions with midazolam in the dog, a selective and sensitive high performance liquid chromatography-tandem mass spectroscopy (HPLC-MS-MS) method has been developed, with sufficient sensitivity to allow analysis of dog plasma samples generated following administration of a clinically relevant dose. The method involves extraction of midazolam and internal standard (flunitrazepam) from dog plasma, using 96-well Oasis MCX solid phase extraction plates. The assay has been validated over a concentration range of 0.1-10 ng/ml and its specificity, accuracy and precision demonstrated. The relative bias of the assay was within +/-15% for all standards with intra- and inter-assay precision (coefficient of variation-%CV) of less than 15%. The assay was applied to the analysis of plasma samples (0.2 ml), generated following intravenous or oral administration of midazolam to male beagle dogs, at a dose level of 0.05 mg/kg, and pharmacokinetic parameters were derived from the resulting data.

Measurement of upper extremity volume in women after axillary dissection for breast cancer.

OBJECTIVE: To determine if 2 methods of calculating upper extremity volume (using arm circumferences) can substitute for water displacement volumetry. DESIGN: Interrater and test-retest reliability and limits of agreement for volume measures. SETTING: University. PARTICIPANTS: Twenty-five women at risk for lymphedema who had undergone axillary lymph node dissection surgery for breast cancer. INTERVENTIONS: Circumference and volume measurements of both upper extremities were taken by 2 physical therapists at an initial visit and by 1 of the therapists 1 week later. MAIN OUTCOME MEASURES: Intraclass correlation coefficients (ICCs) were calculated to analyze measurement reliability. Pearson's product-moment correlation coefficient (r) was used to evaluate the relationship between volumetry and calculated truncated cone volumes. Limits of agreement were calculated to determine the level of agreement between the 2 measurement methods. RESULTS: Interrater and test-retest reliability ICCs for circumferential and volumetric data were .99 and .99, respectively. Pearson's r values were .93 and .97 for the single truncated cone and the summed truncated cone volume calculations, respectively. Limits of agreement (mean +/- 2 standard deviations) were -52 +/- 334mL and -40 +/- 234mL, respectively, between volumetry and the single truncated cone and summed truncated cone calculations. CONCLUSIONS: Calculated and volumetric measurements in this population are both reliable and closely related, but do not agree with each another, and thus should not be used interchangeably.

Improving the time to diagnosis after an abnormal screening mammogram.

INTRODUCTION: Five community-specific interventions to reduce the time to diagnosis after an abnormal breast screen have been evaluated. METHODS: Subjects with abnormal screening mammograms in 1998 were assessed through five community pilot projects (N = 1137) and a control random sample assessed elsewhere in BC (N = 1053). The number, types, dates and physician costs of breast-related interventions after an abnormal screen were compared between pilots and control. RESULTS: The median time to diagnosis for women without a biopsy was reduced from 23 days to 7 days (p = 0.001) in the pilot with facilitated referral to diagnosis. The median time to diagnosis for women with a biopsy was reduced from 57 days to 22-43 days in the pilots. Median physician costs per subject were lower (p = 0.02) in pilots that more frequently used core biopsy to obtain a diagnosis. CONCLUSIONS: Process changes can improve the time to diagnosis after an abnormal breast screen, with similar or lower physician costs per subject. Facilitating the referral process had the greatest impact.

Reliability and validity of the Harris Infant Neuromotor Test.

OBJECTIVE: To examine the reliability and validity of the Harris Infant Neuromotor Test (HINT), a screening tool that can be administered and scored in <30 minutes, with the goal of identifying neuromotor differences in infants aged 3 to 12 months. STUDY DESIGN: Infants, aged 3 to 12 months (n = 54), were assessed in 2 high-risk infant follow-up programs in Vancouver, British Columbia. Inter-rater, test-retest, and intra-rater reliability were examined. Concurrent and predictive validity of the HINT with the Bayley Scales of Infant Development-II (BSID-II) were evaluated by using the Pearson product-moment correlation. RESULTS: Intraclass correlation coefficients for reliability for the Total HINT Score ranged from 0.98 to 0.99. Concurrent validity of the HINT with the BSID-II Mental Scale during the first year was r = -0.73 (P <.01), and with the BSID-II Motor Scale, r = -0.89 (P <.01). The predictive relationships between the HINT and the BSID-II at 17 to 22 months were r = -0.11 for the BSID-II Mental Scale and r = -0.49 (P <.01) for the BSID-II Motor Scale. CONCLUSIONS: The HINT is reliable for screening infant neuromotor performance and has strong concurrent validity with the Bayley-II Mental and Motor Scales. HINT scores during the first year accounted for 24% of the variance of Bayley-II Motor scores at 17 to 22 months.

Clinical practice guidelines for the care and treatment of breast cancer: 11. Lymphedema.

OBJECTIVE: To provide information and recommendations for women and their physicians when making decisions about the management of lymphedema related to breast cancer. OPTIONS: Compression garments, pneumatic compression pumps, massage and physical therapies, other physical therapy modalities, pharmaceutical treatments. OUTCOMES: Symptom control, quality of life, cosmetic results. EVIDENCE: Systematic review of English-language literature retrieved primarily from MEDLINE (1966 to April 2000) and CANCERLIT (1985 to April 2000). Nonsystematic review of breast cancer literature published to October 2000. RECOMMENDATIONS: Pre- and postoperative measurements of both arms are useful in the assessment and diagnosis of lymphedema. Circumferential measurements should be taken at 4 points: the metacarpal-phalangeal joints, the wrists, 10 cm distal to the lateral epicondyles and 15 cm proximal to the lateral epicondyles. Clinicians should elicit symptoms of heaviness, tightness or swelling in the affected arm. A difference of more than 2.0 cm at any of the 4 measurement points may warrant treatment of the lymphedema, provided that tumour involvement of the axilla or brachial plexus, infection and axillary vein thrombosis have been ruled out. Practitioners may want to encourage long-term and consistent use of compression garments by women with lymphedema. One randomized trial has demonstrated a trend in favour of pneumatic compression pumps compared with no treatment. Further randomized trials are required to determine whether pneumatic compression provides additional benefit over compression garments alone. Complex physical therapy, also called complex decongestive physiotherapy, requires further evaluation in randomized trials. In one randomized trial no difference in outcomes was detected between compression garments plus manual lymph drainage versus compression garments alone. Clinical experience supports encouraging patients to consider some practical advice regarding skin care, exercise and body weight. [A patient version of these guidelines appears in Appendix 2.] VALIDATION: An initial draft of this document was developed by a task force sponsored by the BC Cancer Agency. It was updated and revised substantially by a writing committee and then submitted for further review, revision and approval by the Steering Committee for Clinical Practice Guidelines for the Care and Treatment of Breast Cancer. SPONSOR: The steering committee was convened by Health Canada. COMPLETION DATE: October 2000.

Who's listening? Experiences of women with breast cancer in communicating with physicians.

The purpose of this qualitative study was to describe communication behaviors and attitudes of physicians that were most important to women living with breast cancer. Two focus group sessions were conducted, 1 month apart, involving 15 women who were members of a community-based breast cancer support group in Vancouver, British Columbia, Canada. Group dialogue was audiotaped, and notes were taken at each session by the coinvestigators, also members of the support group. Audiotapes, coinvestigators' written notes from the two focus group sessions, and the written homework assignments were used in the qualitative data analysis. Conceptual themes were identified and grouped to discern patterns within the data. The women were asked the following: (a) What were the most helpful things your doctor said or did at the time of your diagnosis? (b) What does a good intervention feel or look like? They were then asked to describe behaviors and attitudes they would like to influence in medical students who might later be communicating with women facing a diagnosis of breast cancer and to indicate which behaviors and attitudes they felt were most important. Women's positive experiences with physicians were characterized by communication based on active listening, awareness of the women's knowledge of their illness, honesty, and partnership. Physicians who showed interest in their patients as persons and who used touch to communicate caring were perceived as supportive communicators. Not surprisingly, there were similarities between the participants' positive experiences with their own physicians and the behaviors and attitudes desired in future physicians. Once again, "listening" was ranked as most important, followed by willingness to discern the individual patient's knowledge level.

Oxidative stress contributes to the anti-proliferative effects of flavone acetic acid on endothelial cells.

The synthetic flavonoid flavone acetic acid (FAA) has anti-tumor activity against a variety of transplanted tumors in mice through mechanisms which likely involve effects on tumor vasculature and the host immune system. The aims of the present in vitro study were to compare the sensitivity of tumor and endothelial cells to FAA treatment and to assess if nitric oxide and superoxide are involved in the FAA-mediated suppression of cell proliferation. FAA at 1 mM concentration was approximately two times more effective in suppressing proliferation of endothelial than tumor cells. The anti-proliferative effect of 1 mM FAA on endothelial cells was partially blocked by inhibitors to various superoxide-producing enzymes (xanthine oxidase, cyclooxygenase, poly-ADP-ribose polymerase, ribonucleotide reductase) and completely inhibited by the direct scavengers of superoxide lucigenin and Tiron. In contrast, inhibitors of nitric oxide were unable to prevent the effects of FAA on proliferation. FAA induced apoptosis of endothelial cells, which was not affected by inhibitors of nitric oxide or superoxide. Our data imply that FAA inhibits proliferation of endothelial cells by a superoxide-dependent mechanism and induces apoptosis by a nitric oxide and superoxide-independent mechanism.

The disposition of saquinavir in normal and P-glycoprotein deficient mice, rats, and in cultured cells.

Protease inhibitors are very effective in treating patients infected with HIV. However, many drugs in this class penetrate poorly into the central nervous system (CNS) and may permit this site to be a sanctuary from which resistant virus can emerge. Previous studies have shown that the protease inhibitor saquinavir (SQV) interacts with the multidrug transport system, P-glycoprotein (P-gp), expressed in epithelial cells in the gut mucosa and at the blood-brain barrier, and thus might affect both the oral absorption and the penetration of SQV into the CNS. To determine whether SQV is a substrate for P-gp, its uptake was determined in cancer cells, which do (Dx5) and do not (MES-SA) express P-gp. The distribution of SQV between brain tissue and plasma was also investigated in rats and in normal and P-gp-deficient mdr1a(-/-) mice. The distribution ratio of SQV in plasma:brain:cerebrospinal fluid was approximately 100:10:0.2 in rats. The accumulation of SQV was enhanced in MES-SA cells (P-gp-negative) versus Dx5 cells (P-gp-positive). Bolus i.v. injection of [(14)C]SQV (2 and 5 mg/kg) into mdr1a(-/-) and normal mice (n = 3 or 4) resulted in 3-fold higher radioactivity in brains from mdr1a(-/-) mice. Similarly, oral administration of [(14)C]SQV (500 mg/kg) resulted in a 5-fold increase in systemic exposure and a 10-fold increase in brain levels in mdr1a(-/-) mice. These data demonstrate that saquinavir is a substrate for P-gp and that this transport system may play a role in limiting oral absorption and CNS exposure to this protease inhibitor.

Challenging the myth of exercise-induced lymphedema following breast cancer: a series of case reports.

Women who have had axillary lymph nodes removed for the management of breast cancer are at increased risk of developing upper extremity lymphedema. Physical therapists, surgeons, and other health professionals have warned these women to avoid vigorous, repetitive, or excessive upper body exercise, believing that such types of exercise might actually induce lymphedema. The purpose of this series of case reports was to challenge that belief by systematically measuring the arm circumferences, across three points in time, of 20 women who had received axillary dissection and who were competing in the vigorous, upper body sport of Dragon Boat racing. Measurably different change was defined as an increase in circumference of the ipsilateral upper extremity at any of the four landmarks of >0.5 inches between Time 1 and Time 2 or between Time 1 and Time 3; only two women showed a measurably different change (5/8 in). Furthermore, none of the women showed a clinically significant difference in arm circumference between the ipsilateral and contralateral extremities at Time 3.