Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study

BACKGROUND

Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions.

AIM

To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study.

METHODS

For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis.

FINDINGS

The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0-29.0 days). Most variation was seen between reporting of a positive COVID-19 polymerase chain reaction (PCR) result to sequence report generation (median 4.0 days, range 2.3-27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT.

CONCLUSION

Integration of pathogen sequencing into diagnostic laboratories may help to improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimize TAT if lower quality samples are removed at an earlier stage.

Safety and tolerability of Pau d' Arco (Tabebuia avellanedae) for primary dysmenorrhea: A single-arm, open-label trial on adults ages 18-45

Objectives

To evaluate the safety and tolerability of encapsulated Tabebuia avellanedae in generally healthy women aged 18-45 with primary dysmenorrhea.

Methods

A single arm, open-label trial was conducted in which 1050 mg/day of encapsulated Tabebuia avellanedae (Pau d'Arco) was administered to twelve healthy women aged 18-45 for eight weeks. The primary outcome was safety and tolerability as measured by standardized adverse events scales and serial collection of laboratory markers to assess general health, prothrombin times, and the presence or absence of anemia. Secondary outcomes included pain intensity, quality of life, and pain interference measured by the Visual Analog Scale (VAS), the Patient-Reported Outcomes Measurement Information System (PROMIS) 29 survey, and the PROMIS Visual Sexual Function and Satisfaction: Interfering Factors survey, respectively. Exploratory outcomes included serum concentration of high-sensitivity C-reactive protein as a marker of systemic inflammation.

Results

Seventy-five percent of participants (n = 9/12) completed the study. Seventy-five percent of study participants (n = 9/12) reported an adverse event, most of which were characterized as mild, and none were determined to be a Food and Drug Administration (FDA) serious adverse event. Most laboratory markers stayed within normal limits throughout the study period with a few clinically mild abnormalities. There was a significant decrease in pain intensity compared to baseline after the first dose (p < .01), after 4 weeks of treatment (p < .01), and after 8 weeks of treatment (p < .01). Over the 8-week intervention period, pain interference, quality of life, and sexual function and satisfaction scores improved nonsignificantly and hs-CRP decreased nonsignificantly.

Conclusions

Tabebuia avellanedae supplementation of 1050 mg/day dose for eight weeks in generally healthy women aged 18-45 with primary dysmenorrhea was generally safe, associated with moderate tolerability, and associated with significant improvements in pain intensity scores. Future studies examining the safety and efficacy of Tabebuia avellanedae on primary dysmenorrhea are warranted.

Alarms, oxygen saturations, and SpO2 averaging time in the NICU

BACKGROUND

Alarm overload is a significant concern in the Neonatal Intensive Care Unit (NICU). Selecting a longer oxygen saturation (SpO2) averaging time will reduce the number of alarms but may mask fluctuations in oxygenation.

OBJECTIVE

Characterize bedside monitor alarms in the NICU and estimate the impact of longer SpO2 averaging time and alarm delay.

METHODS

All bedside monitor alarms were analyzed over a 12-month period in the University of Virginia NICU, using the default averaging time (8 seconds) and SpO2 alarm limits set at 88-95% for infants on supplemental oxygen. In 10 VLBW infants, SpO2 averaging time was lowered to 2 seconds for 24 hours and events of SpO2 out of the target range were estimated with 2-, 8-, or 16-second averaging time, with and without a 15-second alarm delay.

RESULTS

There were 3,263,590 alarms in the unit over 12 months. Low or high SpO2 alarms constituted 79% of the total, and 55% of these events lasted <15 seconds. In 10 infants we estimated that increasing SpO2 averaging time from 2 to 16 seconds would have led to 53% fewer SpO2 alarms but the mean duration of alarms would have been 2.15-fold longer. Adding a 15-second alarm delay to 2-second SpO2 averaging in this analysis decreased SpO2 alarms by 67%.

CONCLUSION

Longer SpO2 averaging times mask the number and severity of events of aberrant oxygenation in preterm infants without decreasing total alarm time. Incorporating an alarm delay with shorter SpO2 averaging times can reduce alarm number and duration, and allow more accurate assessment of oxygenation, which may be important for research into consequences of aberrant oxygenation in this vulnerable population.

Antimicrobial use and resistance in aquaculture: findings of a globally administered survey of aquaculture-allied professionals

There is limited published information regarding antimicrobial use (AMU) and antimicrobial resistance (AMR) in aquaculture. Our objective was to determine the opinions of aquaculture-allied professionals around the world on the frequency of AMU and AMR in common aquatic species. The study questionnaire included five sections: respondent demographics, extent of AMU in aquaculture, frequency of observations of AMR in aquaculture, AMR monitoring and surveillance and antimicrobial susceptibility testing in various jurisdictions. It was administered in English and Spanish to 604 professionals in 25 countries and with varying expertise in aquaculture. The response rate was 33% (199/604). Over half of the participants had >10 years of experience in aquaculture: 70% (140/199) were involved in fish health/clinical work and their primary experience was with salmon, tilapia, trout, shrimp (including prawn) and/or catfish. Tetracycline use was reported by 28%, 46%, 18%, 37% and 9% of respondents working with catfish, salmon, tilapia, trout and shrimp, respectively. Resistance to tetracycline in one or more species of bacteria was reported as 'frequent-to-almost always' for the same aquaculture species by 39%, 28%, 17%, 52% and 36% of respondents, respectively. 'Frequent-to-almost always' use of quinolone was reported by 70% (32/46) and 67% (8/12) of respondents from the United States and Canada, respectively, where quinolone products are not approved for aquaculture, and extra-label fluoroquinolone use is either prohibited (United States) or discouraged (Canada). Similar frequencies of quinolone use were also reported by the majority of respondents from Europe [70% (7/10)] and Asia [90% (9/10)] where labelled indications exist. This baseline information can be used to prioritize research or surveillance for AMU and AMR in aquaculture.

Psychotropic medication use and risk of adverse cardiovascular events in women with suspected coronary artery disease: outcomes from the Women's Ischemia Syndrome Evaluation (WISE) study

OBJECTIVE

This study investigated the relation between psychotropic medication use and adverse cardiovascular (CV) events in women with symptoms of myocardial ischaemia undergoing coronary angiography.

METHOD

Women enrolled in the Women's Ischemia Syndrome Evaluation (WISE) were classified into one of four groups according to their reported antidepressant and anxiolytic medication usage at study intake: (1) no medication (n = 352); (2) anxiolytics only (n = 67); (3) antidepressants only (n = 58); and (4) combined antidepressant and anxiolytics (n = 39). Participants were followed prospectively for the development of adverse CV events (for example, hospitalisations for non-fatal myocardial infarction, stroke, congestive heart failure and unstable angina) or all-cause mortality over a median of 5.9 years.

RESULTS

Use of antidepressant medication was associated with subsequent CV events (HR 2.16, 95% CI 1.21 to 3.93) and death (HR 2.15, 95% CI 1.16 to 3.98) but baseline anxiolytic use alone did not predict subsequent CV events and death. In a final regression model that included demographics, depression and anxiety symptoms, and risk factors for cardiovascular disease, women in the combined medication group (that is, antidepressants and anxiolytics) had higher risk for CV events (HR 3.98, CI 1.74 to 9.10, p = 0.001 and all-cause mortality (HR 4.70, CI 1.7 to 2.97, p = 0.003) compared to those using neither medication. Kaplan-Meier survival curves indicated that there was a significant difference in mortality among the four medication groups (p = 0.001).

CONCLUSIONS

These data suggest that factors related to psychotropic medication such as depression refractory to treatment, or medication use itself, are associated with adverse CV events in women with suspected myocardial ischaemia.

Risk prediction in patients presenting with suspected cardiac pain: the GRACE and TIMI risk scores versus clinical evaluation

BACKGROUND

Identifying which patients presenting with undifferentiated chest pain are at risk of major cardiac events is a major clinical challenge. Clinical evaluation may lack sufficient precision, leading to unnecessary admission or inappropriate discharge. It is uncertain whether risk scores derived from ACS populations apply to unselected patients with chest pain.

AIM

To determine the predictive accuracies of the GRACE risk score, the TIMI risk score and clinical evaluation in unselected patients with suspected cardiac pain.

DESIGN

Prospective observational study.

METHODS

We recruited 347 sequential patients with suspected cardiac pain presenting to a large teaching hospital. The main outcome measures were death, non-fatal myocardial infarction and emergency revascularization, in hospital and at 3 months. Receiver operating characteristic (ROC) curves were plotted for TIMI and GRACE risk scores and clinical evaluation.

RESULTS

Overall 54 patients (15.6%) experienced a major cardiac event (16 deaths, seven myocardial infarctions (MIs), one emergency revascularization) or emergency re-admission (n=30) within 3 months. Both GRACE (p<0.001) and TIMI scores (p<0.001) predicted death/MI/revascularization (and the composite including re-admission), but the GRACE score was superior to the TIMI score for predicting major cardiac events (z=2.05), and both scores were superior to clinical evaluation (ROC areas 0.82, 0.74 and 0.55 respectively). The GRACE score predicted an ACS discharge diagnosis (p<0.001) and duration of hospital stay (p<0.001).

DISCUSSION

In unselected patients presenting with suspected cardiac pain, the GRACE risk score is superior to the TIMI risk score in predicting major cardiac events, and both risk scores are superior to using ECG and troponin findings at presentation.

Experience with use of multiplane transesophageal echocardiography to guide closure of atrial septal defects using the amplatzer device

By providing unlimited imaging planes, multiplane transesophageal echocardiography (MTEE) should improve real-time guidance of interventional procedures. The potential advantages of MTEE in this scenario have not been systematically evaluated. We retrospectively reviewed our experience with MTEE-guided Amplatzer device closure of atrial septal defects (ASDs) MTEE angles used to obtain images for guiding all measurements and maneuvers were recorded. These angles were compared to the range of MTEE angles that are postulated to be available from biplane TEE. Images obtained using MTEE angles from 21 degrees to 70 degrees and from 111 degrees to l59 degrees were defined as only obtainable by MTEE. The MTEE probe was successfully introduced in all (89) patients. Thirteen patients (15%) had multiple defects. Ninety-five devices (5-32 mm in diameter) were deployed. In 66% of patients, balloon sizing and device deployment necessitated imaging planes that are only obtainable by MTEE. All devices were well positioned, with no impingement on inflows or outflows. At follow-up, 79 of 89 (88.7%) patients had no residual ASDs. Each of the remaining 10 patients (11.3%) had a small (<3 mm) residual defect. MTEE played an important role in guiding device closure of ASD, particularly during the phases of balloon sizing and device deployment.

Development of a ubiquitin transfer assay for high throughput screening by fluorescence resonance energy transfer

An assay based on fluorescence resonance energy transfer (FRET) has been developed to screen for ubiquitination inhibitors. The assay measures the transfer of ubiquitin from Ubc4 to HECT protein Rsc 1083. Secondary reagents (streptavidin and antibody to glutathione-S-transferase [GST]), pre-labeled with fluorophores (europium chelate, Eu(3+), and allophycocyanin [APC]), are noncovalently attached via tags (biotin and GST) to the reactants (ubiquitin and Rsc). When Rsc is ubiquitinated, Eu(3+) and APC are brought into close proximity, permitting energy transfer between the two fluorescent labels. FRET was measured as time-resolved fluorescence at the emission wavelength of APC, almost entirely free of nonspecific fluorescence from Eu(3+) and APC. The FRET assay generated a lower ratio of signal to background (8 vs. 31) than an assay for the same ubiquitination step that was developed as a dissociation-enhanced lanthanide fluoroimmunoassay (DELFIA). However, compared to the DELFIA method, use of FRET resulted in higher precision (4% vs. 11% intraplate coefficient of variation). Quenching of fluorescence was minimal when compounds were screened at 10 microg/ml using FRET. Employing a quick and simple homogeneous method, the FRET assay for ubiquitin transfer is ideally suited for high throughput screening.

Structure-activity relationship studies of flavopiridol analogues

Cyclin dependent kinases (CDKs) along with the complementary cyclins form key regulatory checkpoint controls on the cell cycle. Flavopiridol is a synthetic flavone that shows potent and selective cyclin-dependent kinase inhibitory activity. In this paper, we report modifications of the 3-hydroxy-1-methylpiperidinyl (D ring) of flavopiridol and their effect on CDK inhibitory activity.

Correlation of 9G4 idiotope with disease activity in patients with systemic lupus erythematosus

OBJECTIVE

To compare the levels of the 9G4 idiotope (9G4 Id) in systemic lupus erythematosus (SLE) patients with a detailed disease activity index, the British Isles Lupus Assessment Group (BILAG) index, and serological parameters of disease activity by ds DNA antibody levels and serum C3 concentrations.

METHODS

In a cross sectional analysis serum samples from 190 patients with SLE were studied and a further 55 serial bleeds from 14 patients. An enzyme linked immunosorbent assay was used to measure the 9G4 Id, and anti dsDNA and antimyeloperoxidase (MPO) antibodies. The C3 levels were measured by laser nephelometer.

RESULTS

Seventy six of 190 (40%) of the patients tested had raised 9G4 Id levels. In the cross sectional study 9G4 Id levels were found to correlate with disease activity in the BILAG cardiovascular/respiratory renal, and haematological systems and with global BILAG score (p < 0.01). In the serial bleeds 9G4 Id levels correlated with anti-dsDNA antibody and C3 levels, but not with anti-MPO antibodies. No correlations were found with treatment. In six cases the 9G4 Id levels correlated well with global BILAG scores and dsDNA antibody levels. In four cases the BILAG global and 9G4 Id levels alone correlated well.

CONCLUSIONS

Raised levels of the 9G4 Id are present in a substantial proportion of serum samples from patients with lupus, correlate with various aspects of disease activity in SLE. The Id is detectable on anti-dsDNA antibodies, though it must also be present on other immunoglobulins whose specificities remain unknown.

Buying software off the rack. Packages can be the solution to the software shortage

The rapid pace of the computer revolution may well be slowed by the lack of suitable software. Though computers should be increasing business efficiency and productivity, many companies do not have the software that would enable them to enjoy these benefits. Packaged software can close the gap for both large and small companies. Here are some guidelines for making the decision whether to buy a package and for avoiding trouble once the package is installed. The article also describes the features a company should look for in packaged software and the optimal provisions of a software contract.