Predictive value of genomic screening: cross-sectional study of cystic fibrosis in 50,788 electronic health records.

Doubts have been raised about the value of DNA-based screening for low-prevalence monogenic conditions following reports of testing this approach using available electronic health record (EHR) as the sole phenotyping source. We hypothesized that a better model for EHR-focused examination of DNA-based screening is Cystic Fibrosis (CF) since the diagnosis is proactively sought within the healthcare system. We reviewed CFTR variants in 50,778 exomes. In 24 cases with bi-allelic pathogenic CFTR variants, there were 21 true-positives. We considered three cases "potential" false-positives due to limitations in available EHR phenotype data. This genomic screening exhibited a positive predictive value of 87.5%, negative predictive value of 99.9%, sensitivity of 95.5%, and a specificity of 99.9%. Despite EHR-based phenotyping limitations in three cases, the presence or absence of pathogenic CFTR variants has strong predictive value for CF diagnosis when EHR data is used as the sole phenotyping source. Accurate ascertainment of the predictive value of DNA-based screening requires condition-specific phenotyping beyond available EHR data.

EMR documentation of physician-patient communication following genomic counseling for actionable complex disease and pharmacogenomic results.

Genomic risk information for potentially actionable complex diseases and pharmacogenomics communicated through genomic counseling (GC) may motivate physicians and patients to take preventive actions. The Ohio State University-Coriell Personalized Medicine Collaborative is a randomized trial to measure the effects of in-person GC on chronic disease patients provided with multiplex results. Nine personalized genomic risk reports were provided to patients through a web portal, and to physicians via electronic medical record (EMR). Active arm participants (98, 39% female) received GC within 1 month of report viewing; control arm subjects (101, 54% female) could access counseling 3-months post-report viewing. We examined whether GC affected documentation of physician-patient communication by reviewing the first clinical note following the patient's GC visit or report upload to the EMR. Multivariable logistic regression modeling estimated the independent effect of GC on physician-patient communication, as intention to treat (ITT) and per protocol (PP), adjusted for physician educational intervention. Counselees in the active arm had more physician-patient communications than control subjects [ITT, odds ratio (OR): 3.76 (95% confidence interval (CI): 1.38-10.22, p < 0.0094); PP, OR: 5.53 (95% CI: 2.20-13.90, p = 0.0017). In conclusion, GC appreciably affected physician-patient communication following receipt of potentially actionable genomic risk information.

Continuing performance feedback and use of the ultraviolet visible marker to assess cleaning compliance in the healthcare environment.

BACKGROUND: Environmental surfaces have long been suspected to be a reservoir that could contribute to the presence of micro-organisms in healthcare facilities. The objective of this study was to evaluate the effect of providing weekly feedback to the housekeeping staff in improving and sustaining cleaning compliance when using ultraviolet visible marker (UVM) as an audit tool. METHODS: The housekeeping staff selected 90% as the cleaning compliance target. The UVM was applied to the toilet seat, sink, soap dispenser and door knob surfaces within the patient's washrooms on consecutive weekdays. The study included three arms: staff in arm 1 received cleaning compliance feedback throughout the 24-week study period, arm 2 and arm 3 staff received feedback for weeks 13-24 and weeks 1-12, respectively. Feedback was also provided to housekeeping staff by posting graphs on the wards and in the housekeeping office. FINDINGS: A pre-study audit showed 66.9%, 66.5% and 66.4% cleaning compliance for arms 1, 2 and 3 respectively. While receiving weekly feedback, all three arms demonstrated significantly improved cleaning compliance (86.7%, 80.4% and 73.7% for arms 1, 2 and 3, respectively). The use of casual staff may have contributed to difficulty in achieving better cleaning compliance as arms 1, 2 and 3 had 16.1%, 26% and 40.3% of shifts filled by casual staff, respectively. CONCLUSIONS: The use of UVM as an audit tool combined with weekly feedback of results to housekeeping staff resulted in significant, sustained improvement in the overall level of cleaning compliance of housekeeping staff.

Evaluation of an algorithmic approach in comparison with the Illumigene assay for laboratory diagnosis of Clostridium difficile infection.

The following three diagnostic algorithms were evaluated in comparison with the Illumigene assay as a stand-alone test for Clostridium difficile detection: glutamate dehydrogenase antigen screen (GDH) followed by toxin A/B antigen testing (Tox A/B) with the cell cytotoxicity assay for discordant specimens (algorithm 1), GDH followed by the Illumigene (algorithm 2), and GDH followed by Tox A/B with the Illumigene for discordant specimens (algorithm 3). A total of 428 stool specimens submitted to three clinical microbiology laboratories in Manitoba, Canada, for C. difficile detection between June 2011 and April 2012 were included in the study. The prevalence of C. difficile in the stool specimens was 14.7% (63/428) based on toxigenic culture (microbiologic reference standard). The sensitivity and specificity of the Illumigene for C. difficile detection were 73.0% and 99.7%, respectively. The corresponding sensitivities and specificities were 65.1% and 100.0% for algorithm 1, 68.3% and 100.0% for algorithm 2, and 69.8% and 100.0% for algorithm 3. Using algorithm 1, a cell cytotoxicity assay was required for toxin detection in 37% of positive tests, prolonging turnaround time. However, the predictive value of a positive test based on a clinical reference standard (all tests positive or cytotoxigenic culture positive and clinical disease on chart review) was slightly higher with algorithm 1 than with the Illumigene assay as a stand-alone test or as part of an algorithm (algorithms 2 and 3). Based on a reduction in turnaround time, simplicity, and acceptable sensitivity and specificity, we recommend algorithm 2 (screening with the GDH antigen test and confirmatory testing with the Illumigene).

Re-evaluation of rejection criteria for endotracheal tube (ETT) specimens from adult patients.

The purpose of this study was to determine optimal criteria for microbiology laboratory screening of endotracheal tube (ETT) specimens submitted for bacterial culture from adult patients. ETT specimens from adult patients that were received by two microbiology laboratories were prospectively evaluated and subdivided into one of three study arms with the following criteria: <10 squamous epithelial cells (SECs) per low-power field with bacteria seen on Gram staining (arm 1), >10 SECs per low-power field with bacteria seen on Gram staining (arm 2) and <10 SECs per low-power field with no bacteria seen on Gram staining (arm 3). A fourth study arm (>10 SECs per low-power field with no bacteria seen on Gram staining) was planned but this arm was terminated due to the paucity of specimens meeting these criteria. Isolate evaluation was performed using standard microbiology protocols. A limited chart review was undertaken at one of the institutions, only reviewing patients from which a potential pathogen was recovered on culture. In total, 141 ETT specimens were evaluated. A potential respiratory pathogen was recovered from 54, 37 and 10 % of specimens in study arms 1, 2, and 3, respectively (P<0.0001, comparing between arm 1 and arm 3). For the 23 patients included in the chart review from whom a potential pathogen was recovered on culture, respiratory infection was considered to be present in 50 % (6/12) of patients in arm 1, 66.6 % (6/9) of patients in arm 2 and 100 % (2/2) of patients in arm 3. Therapy was rarely altered based on culture results. In this study, the ETT specimens submitted for bacterial culture were of limited benefit to clinicians. The data presented here support the use of an absence of bacteria on Gram staining as a rejection criterion for ETT specimens. The criterion of >10 SECs per low-power field should be further evaluated in a prospective study of patients with an unequivocal clinical diagnosis of pneumonia.

Change in antimicrobial susceptibility of Escherichia coli urinary tract isolates at a single institution over a period of 10 years.

Urinary tract infections are common. Few published studies have demonstrated the change in Escherichia coli urinary isolate antimicrobial susceptibility over time within a given area and (or) population. The purpose of this study was to evaluate the change in susceptibility of E. coli clinical isolates obtained from urine specimens at a single institution over a period of 10 years. The microbiology laboratory information system at St. Boniface Hospital (Winnipeg, Manitoba, Canada) was searched retrospectively from 1 January 2000 to 31 December 2009, for all E. coli isolates from either a midstream or catheter urine source that had susceptibility testing performed. Only one isolate per patient was included during the entire study period. Antimicrobial susceptibility testing was carried out with either a Microscan instrument (pre-April 2004) or a Vitek instrument (May 2004 onwards). In total, 7353 E. coli urinary isolates were included for evaluation. Ciprofloxacin susceptibility declined significantly, from 99% in 2000 to 85% in 2009 (p < 0.0001). A small but statistically significant decline in susceptibility was also observed for ampicillin, cefazolin, trimethoprim-sulfamethoxazole, gentamicin, and nitrofurantoin. These data suggest that certain antimicrobials recommended for the treatment of urinary tract infections (ciprofloxacin, trimethoprim-sulfamethoxazole) may no longer be optimal.

Electroglottogram approximate entropy: a novel single parameter for objective voice assessment.

BACKGROUND: The electroglottogram approximate entropy value is a numerical variable which gives an overall measure of voice quality. It is derived by analysing the complexity of the electroglottogram waveform using regulatory statistics. AIMS: (1) To use electroglottogram approximate entropy to measure voice quality in patients with glottic pathology and in normal subjects, to ascertain whether this parameter can distinguish between pathological and normal voices. (2) To ascertain whether electroglottogram approximate entropy can measure voice change over time within individual subjects. (3) To determine any correlation between electroglottogram approximate entropy and the grade-roughness-breathiness-asthenia-strain scale. METHODS: One hundred and forty-one normal volunteers were recruited to characterise electroglottogram approximate entropy in the normal voice. One hundred and eighty-six patients with glottic squamous cell carcinoma underwent electroglottogram approximate entropy measurement prior to radiotherapy and then three to six months and one year after treatment. Subjects' voices were categorised by a speech therapist using the grade-roughness-breathiness-asthenia-strain scale. RESULTS: The mean electroglottogram approximate entropy of the normal volunteers was 0.302 (range 0.05-0.42). The mean electroglottogram approximate entropy of the glottic squamous cell carcinoma patients was significantly lower prior to treatment, at 0.227 (range 0.001-0.397; p < 0.0005), but improved after radiotherapy to 0.277 at three to six months and 0.282 at one year. Electroglottogram approximate entropy results correlated significantly with grade-roughness-breathiness-asthenia-strain scale results. CONCLUSION: Electroglottogram approximate entropy can be used to assess change in voice quality resulting from glottic morphological abnormality. Electroglottogram approximate entropy values improve as voice quality improves after treatment. Electroglottogram approximate entropy values correlate significantly with grade-roughness-breathiness-asthenia-strain scale results.

Antenatal urologic intervention: current status.

The devastation caused by fetal obstructive uropathy is now well known. At the most severe end of the spectrum of obstructive uropathy not only is the developing kidney damaged but the resultant oligohydra-mnios prevents pulmonary development and causes skeletal defects. The most significant changes are noted in patients with posterior urethral values (PUV). The obvious solution to the problem is to either correct or by pass the obstruction prior to the development of permanent changes. Unfortunately, this simple concept is not easy to apply since it raises numerous ethical, legal, economic and technical problems.

In vitro maturation of clonal CD4+CD8+ cell lines in response to TCR engagement.

Engagement of the TCR on immature CD4+CD8+ (DP) thymocytes by an appropriate peptide/MHC ligand evokes a complex program of maturation known as positive selection. As a result, DP thymocytes are rescued from programmed cell death, become committed to the CD4 or CD8 lineage, extinguish expression of V(D)J recombinase activity, and undergo further maturation. We describe here a panel of DP thymic lymphoma cell lines that, in response to in vitro TCR engagement, undergo many of the TCR-beta-induced maturation events that have been reported to accompany positive selection of DP thymocytes in vivo. These events include increased expression of CD5, CD69, CD45, TCR-alpha, and MHC class I, and decreased expression of Thy-1 and heat-stable Ag. In addition, we observed TCR-induced expression of the bcl-2 gene, a well described inhibitor of programmed cell death. Finally, TCR engagement decreased expression of recombinase-activating genes and terminal deoxynucleotidal transferase genes, as well as V(D)J recombinase activity. However, TCR engagement did not elicit demonstrable CD4/CD8 lineage commitment. These observations suggest that engagement of the TCR on these DP cell lines elicits multiple maturation events that are part of the positive selection developmental program, but not CD4/CD8 lineage commitment. Thus, these DP cell lines provide the opportunity to elucidate molecular mechanisms of maturation and CD4/CD8 lineage commitment in vitro.