Performance evaluation in cataract surgery with an ensemble of 2D-3D convolutional neural networks

An important part of surgical training in ophthalmology is understanding how to proficiently perform cataract surgery. Operating skill in cataract surgery is typically assessed by real-time or video-based expert review using a rating scale. This is time-consuming, subjective and labour-intensive. A typical trainee graduates with over 100 complete surgeries, each of which requires review by the surgical educators. Due to the consistently repetitive nature of this task, it lends itself well to machine learning-based evaluation. Recent studies utilize deep learning models trained on tool motion trajectories obtained using additional equipment or robotic systems. However, the process of tool recognition by extracting frames from the videos to perform phase recognition followed by skill assessment is exhaustive. This project proposes a deep learning model for skill evaluation using raw surgery videos that is cost-effective and end-to-end trainable. An advanced ensemble of convolutional neural network models is leveraged to model technical skills in cataract surgeries and is evaluated using a large dataset comprising almost 200 surgical trials. The highest accuracy of 0.8494 is observed on the phacoemulsification step data. Our model yielded an average accuracy of 0.8200 and an average AUC score of 0.8800 for all four phase datasets of cataract surgery proving its robustness against different data. The proposed ensemble model with 2D and 3D convolutional neural networks demonstrated a promising result without using tool motion trajectories to evaluate surgery expertise.

Change in economy of ultrasound probe motion among general medicine trainees

OBJECTIVES

To observe change in economy of 9 ultrasound probe movement metrics among internal medicine trainees during a 5-day training course in cardiac point of care ultrasound (POCUS).

METHODS

We used a novel probe tracking device to record nine features of ultrasound probe movement, while trainees and experts optimized ultrasound clips on the same volunteer patients. These features included translational movements, gyroscopic movements (titling, rocking, and rotation), smoothness, total path length, and scanning time. We determined the adjusted difference between each trainee's movements and the mean value of the experts' movements for each patient. We then used a mixed effects model to trend average the adjusted differences between trainees and experts throughout the 5 days of the course.

RESULTS

Fifteen trainees were enrolled. Three echocardiographer technicians and the course director served as experts. Across 16 unique patients, 294 ultrasound clips were acquired. For all 9 movements, the adjusted difference between trainees and experts narrowed day-to-day (p value < 0.05), suggesting ongoing improvement during training. By the last day of the course, there were no statistically significant differences between trainees and experts in translational movement, gyroscopic movement, smoothness, or total path length; yet on average trainees took 28 s (95% CI [14.7-40.3] seconds) more to acquire a clip.

CONCLUSIONS

We detected improved ultrasound probe motion economy among internal medicine trainees during a 5-day training course in cardiac POCUS using an inexpensive probe tracking device. Objectively quantifying probe motion economy may help assess a trainee's level of proficiency in this skill and individualize their POCUS training.

Preoperative Oesophagogastroduodenoscopy and the Effect on Bariatric Surgery: a Systematic Review and Meta-Analysis

Preoperative oesophagogastroduodenoscopy (OGD) in bariatric surgery remains a controversial topic, with a large variety in practice globally. An electronic database search of Medline, Embase and PubMed was performed in an aim to categorise the findings of preoperative endoscopies in bariatric patients. A total of 47 studies were included in this meta-analysis resulting in 23,368 patients being assessed. Of patients assessed, 40.8% were found to have no novel findings, 39.7% had novel findings which did not affect surgical planning, 19.8% had findings that affected their surgery and 0.3% were ruled to not be suitable for bariatric surgery. Preoperative OGD is altering surgical planning in one-fifth of patients; however, further comparative studies are required to determine if each patient should undergo this procedure especially if asymptomatic.

Evaluation of the diagnostic performance of the urine dipstick test for the detection of urinary tract infections in patients treated in Kenyan hospitals

Introduction

Culture is the gold-standard diagnosis for urinary tract infections (UTIs). However, most hospitals in low-resource countries lack adequately equipped laboratories and relevant expertise to perform culture and, therefore, rely heavily on dipstick tests for UTI diagnosis.

Research gap

In many Kenyan hospitals, routine evaluations are rarely done to assess the accuracy of popular screening tests such as the dipstick test. As such, there is a substantial risk of misdiagnosis emanating from inaccuracy in proxy screening tests. This may result in misuse, under-use or over-use of antimicrobials.

Aim

The present study aimed to assess the accuracy of the urine dipstick test as a proxy for the diagnosis of UTIs in selected Kenyan hospitals.

Methods

A hospital-based cross-sectional method was used. The utility of dipstick in the diagnosis of UTIs was assessed using midstream urine against culture as the gold standard.

Results

The dipstick test predicted 1416 positive UTIs, but only 1027 were confirmed positive by culture, translating to a prevalence of 54.1 %. The sensitivity of the dipstick test was better when leucocytes and nitrite tests were combined (63.1 %) than when the two tests were separate (62.6 and 50.7 %, respectively). Similarly, the two tests combined had a better positive predictive value (87.0 %) than either test alone. The nitrite test had the best specificity (89.8 %) and negative predictive value (97.4 %) than leucocytes esterase (L.E) or both tests combined. In addition, sensitivity in samples from inpatients (69.2 %) was higher than from outpatients (62.7 %). Furthermore, the dipstick test had a better sensitivity and positive predictive value among female (66.0 and 88.6 %) than male patients (44.3 and 73.9 %). Among the various patient age groups, the dipstick test's sensitivity and positive predictive value were exceptionally high in patients ≥75 years old (87.5 and 93.3 %).

Conclusion

Discrepancies in prevalence from the urine dipstick test and culture, the gold standard, indicate dipstick test inadequacy for accurate UTI diagnosis. The finding also demonstrates the need for urine culture for accurate UTI diagnosis. However, considering it is not always possible to perform a culture, especially in low-resource settings, future studies are needed to combine specific UTI symptoms and dipstick results to assess possible increases in the test's sensitivity. There is also a need to develop readily available and affordable algorithms that can detect UTIs where culture is not available.

POS1106 MEDIATORS OF THE EFFECT OF THERAPEUTIC EXERCISE ON PAIN AND FUNCTION IN PATIENTS WITH KNEE AND HIP OSTEOARTHRITIS; AN INDIVIDUAL PATIENT DATA MEDIATION STUDY FROM THE OA TRIAL BANK

Background

Currently, there is no cure for osteoarthritis (OA). Therapeutic exercise is recommended in all international guidelines to improve pain and function (1). However, randomised controlled trials (RCTs) investigating therapeutic exercise showed that, on average, effect sizes are small to moderate compared to non-exercise controls (2-3). Better knowledge about how therapeutic exercise works to improve pain and function could help improve the design and delivery of future therapeutic exercise interventions and potentially improve patient outcomes.

Objectives

To evaluate the mediating effects of 1) muscle strength, proprioception, and range of motion (ROM) among patients with knee OA, and 2) muscle strength among patients with hip OA, using the procedures established for Individual Participant Data (IPD) analyses by the OA Trial Bank.

Methods

Relevant IPD were sought from all published RCTs comparing therapeutic exercise to a non-exercise control group among people with knee and/or hip OA, using previously published methods (4). For each potential mediator separately, the effect of exercise on the absolute change in pain/function directly after the intervention was determined, controlling for the relative change in mediator under investigation and potential mediator-outcome confounders, using the ‘counterfactual framework’ (5). Next, the effect of exercise on the relative change in the mediator was determined. The percentage mediated was calculated by dividing the natural indirect effect by the total effect.

Results

We obtained IPD from 12 RCTs and 1407 participants (knee OA = 1113; hip OA n=294) that were eligible for inclusion in one or more mediation analyses. Therapeutic exercise showed a significant effect on the relative change in muscle strength in knee OA, but not for proprioception or ROM in knee OA, nor for muscle strength in hip OA. Of all mediators, only the change in muscle strength had a significant effect on the change in pain in knee OA, and on function in knee OA and in hip OA. The percentage mediated for each mediator and each outcome was small (5.3% or less, see Table 1).

Table 1.

Percentage mediated for all potential mediators, by outcome and joint.

Knee OAPainKnee OAFunctionHip OAPainHip OAFunctionMuscle strength2.4%2.3%absentabsentProprioceptionabsent0.2%--Range of motion1.8%5.3%--

‘absent’: no percentage mediated calculated, since direct and indirect effect had opposite directions.

‘-‘: factors not considered a potential mediator for therapeutic exercise in hip OA.

Conclusion

In the first IPD mediation analysis to our knowledge of this scale, muscle strength, proprioception and ROM did mediate the effect of therapeutic exercise for pain and function in knee OA, but only to a very small degree. We observed no such mediating effect of muscle strength for therapeutic exercise in patients with hip OA. The challenge remains to better understand the key mechanisms of action of therapeutic exercise for knee and hip OA, so that exercise interventions can be designed and delivered to target these and therewith optimise the effects for patients.

References

[1]Bierma-Zeinstra S, et al. Nonpharmacological and nonsurgical approaches in OA. Best Pract Res Clin Rheumatol. 2020 Apr;34(2):101564.

[2]Fransen M, et al. Exercise for osteoarthritis of the knee. Cochrane Database Syst Rev. 2015 Jan 9;1:CD004376.

[3]Fransen M, et al. Exercise for osteoarthritis of the hip. Cochrane Database Syst Rev. 2014 Apr 22(4):CD007912.

[4]Holden MA, et al. Subgrouping and TargetEd Exercise pRogrammes for knee and hip OsteoArthritis (STEER OA): a systematic review update and individual participant data meta-analysis protocol. BMJ Open. 2017 Dec 22;7(12):e018971.

[5]VanderWeele TJ, Vansteelandt S. Mediation Analysis with Multiple Mediators. Epidemiol Methods. 2014 Jan;2(1):95-115.

Acknowledgements

We thank all members of the OA Trial Bank Exercise Collaborative, who shared IPD with the OA Trial Bank/STEER OA for making this study possible.

Disclosure of Interests

Jos Runhaar Grant/research support from: Fellowship from the Foundation for Research in Rheumatology (FOREUM), Melanie Holden Grant/research support from: Grant from the Chartered Society of Physiotherapy Charitable Trust (grant no PRF/16/A07), and the National Institute for Health Research (NIHR) School of Primary Care Research (grant no 531), Miriam Hattle: None declared, Johny Quicke Grant/research support from: JQ is part-funded by an NIHR CRN West Midlands Research Scholarship and part funded by the Haywood Foundation, Richard Riley: None declared, Emma Healey Grant/research support from: part funded by the National Institute for Health Research (NIHR) Applied Research Collaboration (ARC) West Midlands., Danielle van der Windt: None declared, Krysia Dziedzic: None declared, Marienke Van Middelkoop: None declared, S.M.A. Bierma-Zeinstra Grant/research support from: OA Trial Bank received long-term funding by the Dutch Arthritis Association, Nadine Foster: None declared

Characterizing the biomechanical differences between novice and expert point-of-care ultrasound practitioners using a low-cost gyroscope and accelerometer integrated sensor: A pilot study

INTRODUCTION

Point-of-care ultrasound (POCUS) has become an important diagnostic tool in acute care medicine; however, little is known about the biomechanical differences between novice and expert practitioners.

METHODS

A low-cost ($50 CAD) gyroscope and accelerometer integrated sensor was assembled and affixed to an ultrasound probe. Seventeen participants, nine novices and eight experts, were recruited to perform three abdominal and four cardiac scans on a standardized patient. Participant demographics, time per scan, average acceleration, average angular velocity, decay in acceleration and angular velocity over time, and frequency of probe movements were analyzed. Video capture with blinded video review was scored.

RESULTS

On video review, experts had higher image optimization and acquisition scores for both abdominal and cardiac scans. Experts had shorter scan times for abdominal (7 s vs. 26 s, p = 0.003) and cardiac (11 s vs. 26 s, p < 0.001) scans. There was no difference in average acceleration (g) between novices and experts performing abdominal (1.02 vs. 1.01, p = 0.50) and cardiac (1.01 vs. 1.01, p = 0.45) scans. Experts had lower angular velocity (°/s) for abdominal scans (10.00 vs. 18.73, p < 0.001) and cardiac scans (15.61 vs. 20.33, p = 0.02) There was a greater decay in acceleration over time for experts performing cardiac scans compared to novices (-0.194 vs. -0.050, p = 0.03) but not for abdominal scans or when measuring angular velocity. The frequency of movements (Hz) was higher for novices compared to experts for abdominal (16.68 vs. 13.79, p < 0.001) and cardiac (17.60 vs. 13.63, p = 0.002) scans.

DISCUSSION

This study supports the feasibility of a low-cost gyroscope and accelerometer integrated sensor to quantify the biomechanics of POCUS. It may also support the concept of "window shopping" as a method by which experts obtain abdominal and cardiac views, where sliding is used to find an acoustic window, then smaller rocking and tilting probe movements are used to refine the image.

Genomic Analysis of Global Staphylococcus argenteus Strains Reveals Distinct Lineages With Differing Virulence and Antibiotic Resistance Gene Content

Infections due to Staphylococcus argenteus have been increasingly reported worldwide and the microbe cannot be distinguished from Staphylococcus aureus by standard methods. Its complement of virulence determinants and antibiotic resistance genes remain unclear, and how far these are distinct from those produced by S. aureus remains undetermined. In order to address these uncertainties, we have collected 132 publicly available sequences from fourteen different countries, including the United Kingdom, between 2005 and 2018 to study the global genetic structure of the population. We have compared the genomes for antibiotic resistance genes, virulence determinants and mobile genetic elements such as phages, pathogenicity islands and presence of plasmid groups between different clades. 20% (n = 26) isolates were methicillin resistant harboring a mecA gene and 88% were penicillin resistant, harboring the blaZ gene. ST2250 was identified as the most frequent strain, but ST1223, which was the second largest group, contained a marginally larger number of virulence genes compared to the other STs. Novel S. argenteus pathogenicity islands were identified in our isolates harboring tsst-1, seb, sec3, ear, selk, selq toxin genes, as well as chromosomal clusters of enterotoxin and superantigen-like genes. Strain-specific type I modification systems were widespread which would limit interstrain transfer of genetic material. In addition, ST2250 possessed a CRISPR/Cas system, lacking in most other STs. S. argenteus possesses important genetic differences from S. aureus, as well as between different STs, with the potential to produce distinct clinical manifestations.

Use of Lateral Flow Immunoassay to Characterize SARS-CoV-2 RBD-Specific Antibodies and Their Ability to React with the UK, SA and BR P.1 Variant RBDs

Identifying anti-spike antibodies that exhibit strong neutralizing activity against current dominant circulating variants, and antibodies that are escaped by these variants, has important implications in the development of therapeutic and diagnostic solutions and in improving understanding of the humoral response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We characterized seven anti-SARS-CoV-2 receptor binding domain (RBD) antibodies for binding activity, pairing capability, and neutralization activity to SARS-CoV-2 and three variant RBDs via lateral flow immunoassays. The results allowed us to group these antibodies into three distinct epitope bins. Our studies showed that two antibodies had broadly potent neutralizing activity against SARS-CoV-2 and these variant RBDs and that one antibody did not neutralize the South African (SA) and Brazilian P.1 (BR P.1) RBDs. The antibody escaped by the SA and BR P.1 RBDs retained binding activity to SA and BR P.1 RBDs but was unable to induce neutralization. We demonstrated that lateral flow immunoassay could be a rapid and effective tool for antibody characterization, including epitope classification and antibody neutralization kinetics. The potential contributions of the mutations (N501Y, E484K, and K417N/T) contained in these variants' RBDs to the antibody pairing capability, neutralization activity, and therapeutic antibody targeting strategy are discussed.

Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments

Intertidal systems are complex and dynamic environments with many interacting factors influencing biochemical characteristics and microbial communities. One key factor are the actions of resident fauna, many of which are regarded as ecosystem engineers because of their bioturbation, bioirrigation and sediment stabilising activities. The purpose of this investigation was to elucidate the evolutionary implications of the ecosystem engineering process by identifying, if any, aspects that act as selection pressures upon microbial communities. A mesocosm study was performed using the well characterised intertidal ecosystem engineers Corophium volutator, Hediste diversicolor, and microphytobenthos, in addition to manual turbation of sediments to compare effects of bioturbation, bioirrigation and stabilisation. A range of sediment functions and biogeochemical gradients were measured in conjunction with 16S rRNA sequencing and diatom taxonomy, with downstream bacterial metagenome function prediction, to identify selection pressures that incited change to microbial community composition and function. Bacterial communities were predominantly Proteobacteria, with the relative abundance of Bacteroidetes, Alphaproteobacteria and Verrucomicrobia being partially displaced by Deltaproteobacteria, Acidobacteria and Chloroflexi as dissolved oxygen concentration and redox potential decreased. Bacterial community composition was driven strongly by biogeochemistry; surface communities were affected by a combination of sediment functions and overlying water turbidity, and subsurface communities by biogeochemical gradients driven by sediment reworking. Diatom communities were dominated by Nitzschia laevis and Achnanthes sp., and assemblage composition was influenced by overlying water turbidity (manual or biogenic) rather than direct infaunal influences such as grazing.

A highly conserved complete accessory Escherichia coli type III secretion system 2 is widespread in bloodstream isolates of the ST69 lineage

Bacterial type III secretion systems (T3SSs) play an important role in pathogenesis of Gram-negative infections. Enteropathogenic and enterohemorrhagic Escherichia coli contain a well-defined T3SS but in addition a second T3SS termed E. coli T3SS 2 (ETT2) has been described in a number of strains of E. coli. The majority of pathogenic E. coli contain elements of a genetic locus encoding ETT2, but which has undergone significant mutational attrition rendering it without predicted function. Only a very few strains have been reported to contain an intact ETT2 locus. To investigate the occurrence of the ETT2 locus in strains of human pathogenic E. coli, we carried out genomic sequencing of 162 isolates obtained from patient blood cultures in Scotland. We found that 22 of 26 sequence type (ST) 69 isolates from this collection contained an intact ETT2 together with an associated eip locus which encodes putative secreted ETT2 effectors as well as eilA, a gene encoding a putative transcriptional regulator of ETT2 associated genes. Using a reporter gene for eilA activation, we defined conditions under which this gene was differentially activated. Analysis of published E. coli genomes with worldwide representation showed that ST69 contained an intact ETT2 in these strains as well. The conservation of the genes encoding ETT2 in human pathogenic ST69 strains strongly suggests it has importance in infection, although its exact functional role remains obscure.

Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections

Bacteraemia caused by Escherichia coli is a growing problem with a significant mortality. The factors that influence the acquisition and outcome of these infections are not clear. Here, we have linked detailed genetic data from the whole-genome sequencing of 162 bacteraemic isolates collected in Scotland, UK, in 2013–2015, with clinical data in order to delineate bacterial and host factors that influence the acquisition in hospital or the community, outcome and antibiotic resistance. We identified four major sequence types (STs) in these isolates: ST131, ST69, ST73 and ST95. Nearly 50 % of the bacteraemic isolates had a urinary origin. ST69 was genetically distinct from the other STs, with significantly less sharing of accessory genes and with a distinct plasmid population. Virulence genes were widespread and diversely distributed between the dominant STs. ST131 was significantly associated with hospital-associated infections (HAIs), and ST69 with those from the community. However, there was no association of ST with outcome, although patients with HAI had a higher immediate mortality compared to those with community-associated infections (CAIs). Genome-wide association studies revealed genes involved in antibiotic persistence as significantly associated with HAIs and those encoding elements of a type VI secretion system with CAIs. Antibiotic resistance was common, and there were networks of correlated resistance genes and phenotypic antibiotic resistance. This study has revealed the complex interactions between the genotype of E. coli and its ability to cause bacteraemia, and some of the determinants influencing hospital or community acquisition. In part, these are shaped by antibiotic usage, but strain-specific factors are also important.

Sonographic Accuracy as a Novel Tool for Point-of-care Ultrasound Competency Assessment

OBJECTIVES

The Focused Assessment with Sonography in Trauma (FAST) is a point-of-care ultrasound (PoCUS) study that is routine in trauma patient assessment. Many organizations have published training guidelines, which grant competency through the completion of a fixed number of observed scans. This approach is incongruent with current trends in competency-based medical education. We aim to objectively quantify probe motion and user accuracy to differentiate groups of PoCUS operators.

METHODS

Emergency medicine residents were recruited in two groups. The novice group (n = 15) had limited PoCUS experience, whereas the intermediate group (n = 14) had completed at least 50 supervised FAST examinations. Both groups underwent assessment on a live human model. Residents from the novice group returned (n = 9) after completing a curriculum and repeated the assessment using the identical experimental construct.

RESULTS

Significant differences (p < 0.05) were found between the novice and both the intermediate and the novice returned groups in time, path length, and points of interest (POIs) scanned. Novices required more time to complete the full examination (290.82 seconds vs. 197.41 seconds vs. 271.79 seconds), utilized more motion (9392.07 mm vs. 4052.73 mm vs. 4985.05 mm), and imaged fewer POIs (48.13% vs. 95.00% vs. 100.00%) when compared to intermediates and returning novices, respectively. No difference was found between the intermediate and novice returned groups for the complete examination. Spearman's correlation was calculated between variables within each group. Correlations between time and path length were statistically significant (p < 0.05) with novice, intermediate, and novice returned values of 0.67, 0.65, and 0.90. Interestingly, neither time nor path length consistently correlated with POIs scanned in any group.

CONCLUSION

Differences in probe motion efficiency and POIs scanned between novices and intermediate or returning novice users show promise for use as a quantitative objective assessment tool. Unlike in surgical literature, accuracy did not correlate with path length or time to examination completion.

Neutrophil function and cardiopulmonary bypass in humans. The effects of glucose and non-glucose containing bypass pump priming fluids

Defective polymorphonuclear neutrophil function during cardiopulmonary bypass (CPB) has been implicated as a cause of postoperative infection following open-heart surgery. Neutrophil function is known to be impaired in poorly controlled diabetics with elevations of blood glucose concentrations of the order which occur frequently during CPB when glucose containing priming fluids are used. Neutrophil function, as measured by bactericidal assay, and neutrophil and whole blood luminol dependent chemiluminescence, was studied in two groups of 1 2 patients undergoing coronary artery bypass graft surgery. Patients received either a glucose or non-glucose containing bypass pump-priming fluid. Postoperatively neutrophil luminol-dependent chemiluminescence was significantly increased in both groups (glucose prime groups p < 0.01, non-glucose prime group p < 0.01). Whole blood chemiluminescence was increased significantly intra and postoperatively in the glucose prime group ( p < 0.02, p < 0.02 respectively) but the increase was not significant in the non-glucose prime group. Bactericidal activity remained unchanged during and after surgery in both groups (mean bactericidal index intraoperatively 96.4 glucose group, 96.2 non-glucose group; postoperatively 99.7 glucose group, 99.7 non-glucose group). These data suggest that glucose containing bypass priming fluids do not modulate significantly the function of circulating neutrophils after CPB. Neutrophil function was not decreased after surgery, and other factors may be responsible for the reported higher incidence of bacterial infection after CPB.

Examination of Learning Trajectories for Simulated Lumbar Puncture Training Using Hand Motion Analysis

OBJECTIVES

A prospective cohort study was conducted using hand motion analysis (HMA) to assess the acquisition and retention of technical proficiency among first-year medical students learning the lumbar puncture (LP) skill in a simulated setting.

METHODS

Twenty-five subjects attended three or four simulation sessions at 6-week intervals. The initial session consisted of an introduction to the procedure and a baseline HMA assessment. This was followed by a session involving deliberate practice and evaluation using HMA. Subject HMA metrics were followed over time and compared to performance benchmarks to determine the volume of practice required to achieve and maintain technical proficiency in the simulated setting. Performance benchmarks were derived from the assessment of experts using HMA.

RESULTS

Subject baseline metrics were significantly different from expert (p < 0.01). At the outset of session 2, none of the subjects achieved the performance benchmarks. At the outset of sessions 3 and 4, 40 and 60% of subjects, respectively, demonstrated retention of technical proficiency. However, there was evidence of significant skill erosion between sessions (p < 0.01). The mean number of practice attempts required to achieve technical proficiency declined between sessions. Regression analysis indicated that there was a significant training effect for all students (overall negative slopes) over time. When examining the group as a whole, the speed at which students reached the expert benchmark was not significantly associated with number of practices in the first three sessions, although for some individuals these factors did appear associated. A total of 76% of subjects retained technical proficiency by session 4 and required a mean of 14 practices (range = 5 to 19).

CONCLUSIONS

These results show that the majority of students require three to four sessions of deliberate practice to achieve a sustainable level of proficiency in the LP procedure. There is considerable variation in learning progression and retention of technical proficiency. These results have important implications for the design and resource requirements of a competency-based medical education program targeting LP training.

Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus

Bacterial virulence is a multifaceted trait where the interactions between pathogen and host factors affect the severity and outcome of the infection. Toxin secretion is central to the biology of many bacterial pathogens and is widely accepted as playing a crucial role in disease pathology. To understand the relationship between toxicity and bacterial virulence in greater depth, we studied two sequenced collections of the major human pathogen Staphylococcus aureus and found an unexpected inverse correlation between bacterial toxicity and disease severity. By applying a functional genomics approach, we identified several novel toxicity-affecting loci responsible for the wide range in toxic phenotypes observed within these collections. To understand the apparent higher propensity of low toxicity isolates to cause bacteraemia, we performed several functional assays, and our findings suggest that within-host fitness differences between high- and low-toxicity isolates in human serum is a contributing factor. As invasive infections, such as bacteraemia, limit the opportunities for onward transmission, highly toxic strains could gain an additional between-host fitness advantage, potentially contributing to the maintenance of toxicity at the population level. Our results clearly demonstrate how evolutionary trade-offs between toxicity, relative fitness, and transmissibility are critical for understanding the multifaceted nature of bacterial virulence.

This study shows that, contrary to expectation, toxin secretion inversely correlates with disease severity for the major human pathogen Staphylococcus aureus.

Global efforts to counter the growing problem of antibiotic resistance and develop alternative treatment strategies rely on a fuller understanding of when and why opportunistic pathogens cause disease. Recent advances in DNA sequencing technologies have opened up new opportunities to study infectious organisms, yet identifying the genetic variants that explain differences in disease remains challenging. Here we aimed to understand the complex relationship between toxicity—a known risk factor for disease in many bacteria—and infection severity for the major human pathogen S. aureus. Against expectations, we found that the bacteria that caused the most severe disease were the least toxic strains. We were able to determine the mutations responsible for the differences in toxicity and identified a number of novel toxicity-affecting genes. We further discovered that bacterial fitness in human serum could explain the unexpected association of low-toxicity isolates with severe, invasive disease. Invasive S. aureus infections are usually considered a dead end for these bacteria, as these infections are rarely transmitted to another person. Here we show using a simple mathematical model that this might in fact favour transmission of highly toxic bacteria on a population level and thus contribute to their global success. Our work therefore highlights the complexity of bacterial infection and should aid in devising new treatment and control strategies against this important pathogen.

T Cell Immunity to the Alkyl Hydroperoxide Reductase of Burkholderia pseudomallei: A Correlate of Disease Outcome in Acute Melioidosis

There is an urgent need for a better understanding of adaptive immunity to Burkholderia pseudomallei, the causative agent of melioidosis that is frequently associated with sepsis or death in patients in Southeast Asia and Northern Australia. The imperative to identify vaccine targets is driven both by the public health agenda in these regions and biological threat concerns. In several intracellular bacterial pathogens, alkyl hydroperoxidase reductases are upregulated as part of the response to host oxidative stress, and they can stimulate strong adaptive immunity. We show that alkyl hydroperoxidase reductase (AhpC) of B. pseudomallei is strongly immunogenic for T cells of ‘humanized’ HLA transgenic mice and seropositive human donors. Some T cell epitopes, such as p6, are able to bind diverse HLA class II heterodimers and stimulate strong T cell immunity in mice and humans. Importantly, patients with acute melioidosis who survive infection show stronger T cell responses to AhpC relative to those who do not. Although the sequence of AhpC is virtually invariant among global B. pseudomallei clinical isolates, a Cambodian isolate varies only in C-terminal truncation of the p6 T cell epitope, raising the possibility of selection by host immunity. This variant peptide is virtually unable to stimulate T cell immunity. For an infection in which there has been debate about centrality of T cell immunity in defense, these observations support a role for T cell immunity to AhpC in disease protection.

The development and validation of hand motion analysis to evaluate competency in central line catheterization

OBJECTIVES

Traditionally, technical skills proficiency has been assessed by direct observation. While direct observation and feedback are essential components in technical skills learning, they demand considerable investment of faculty time, and as an assessment tool, direct observation is inherently subjective and has been criticized as unreliable. The purpose of this study was to determine if quantitative electromagnetic motion tracking is feasible and can discriminate between experts and nonexperts during simulated ultrasound (US)-guided insertion of a central venous catheter (CVC) guidewire.

METHODS

Ten nonexperts (junior emergency medicine residents) and 10 experts (critical care fellows or attending physicians) were recruited. Electromagnetic sensor probes were used to capture hand motion during an US-guided internal jugular cannulation on a standardized manikin. Hand, US, and needle motion were analyzed for the following metrics: total path length, total time, translational movements, and rotational movements. Subjects were also videotaped and evaluated using a modified, validated global rating scale (GRS) by a blinded expert.

RESULTS

There was a significant difference in almost all examined motion parameters between experts and nonexperts. Experts took 66% less time (50.2 seconds vs. 148.7 seconds, p < 0.001) and had significantly less right-hand and US motion (total path length and translational and rotational movements). Left-hand total path length was the only parameter that was not significantly different between groups. Concurrent validity of motion parameters was established by strong correlations (r2 > 0.74) to a previously published, modified GRS.

CONCLUSIONS

Electromagnetic hand and instrument motion analysis is technically feasible for assessing competence in US-guided insertion of a CVC guidewire in a simulation setting. In showing that it discriminates between the performances of nonexperts and experts, this study has provided evidence for construct validity. It also shows excellent correlation with a modified version of a previously validated GRS, providing evidence of concurrent validity.

Assessment of lumbar puncture skill in experts and nonexperts using checklists and quantitative tracking of needle trajectories: implications for competency-based medical education

CONSTRUCT: With the current shift toward competency-based education, rigorous assessment tools are needed for procedurally based tasks.

BACKGROUND

Multiple tools exist to evaluate procedural skills, each with specific weaknesses.

APPROACH

We sought to determine if quantitative needle tracking could be used as a measure of lumbar puncture (LP) performance and added discriminatory value to a dichotomous checklist. Thirty-two medical students were divided into 2 groups. One group was asked to practice an LP once (single practice [SP]) and the other 5 times (multiple practice [MP]). Experts (attending ER physicians, senior ER residents, and a junior anesthesia resident) were used as comparators. Medical students were assessed again at 1 month to assess skill retention. Groups were assessed performing an LP with an electromagnetic tracking device that allows the needle's 3-dimensional movements to be captured and analyzed, and a dichotomous checklist.

RESULTS

Quantitative needle metrics as assessed by electromagnetic tracking showed a decreasing trend in needle movement distance with practice and with experience. The SP group made significantly more checklist mistakes initially as compared to the MP group (1.2 vs. 0.3, p <.05). At 1 month, there was a significant increase in both groups' mistakes (SP 3.4 vs. MP 1.3, p =.01). No correlation existed between individuals' needle motion and checklist mistakes.

CONCLUSIONS

These findings suggest that quantitative needle tracking identifies students who struggle with needle insertion but are successful at completing the dichotomous checklist.

Innate immunity. A Spaetzle-like role for nerve growth factor β in vertebrate immunity to Staphylococcus aureus

Many key components of innate immunity to infection are shared between Drosophila and humans. However, the fly Toll ligand Spaetzle is not thought to have a vertebrate equivalent. We have found that the structurally related cystine-knot protein, nerve growth factor β (NGFβ), plays an unexpected Spaetzle-like role in immunity to Staphylococcus aureus infection in chordates. Deleterious mutations of either human NGFβ or its high-affinity receptor tropomyosin-related kinase receptor A (TRKA) were associated with severe S. aureus infections. NGFβ was released by macrophages in response to S. aureus exoproteins through activation of the NOD-like receptors NLRP3 and NLRP4 and enhanced phagocytosis and superoxide-dependent killing, stimulated proinflammatory cytokine production, and promoted calcium-dependent neutrophil recruitment. TrkA knockdown in zebrafish increased susceptibility to S. aureus infection, confirming an evolutionarily conserved role for NGFβ-TRKA signaling in pathogen-specific host immunity.

Fish oil supplementation induces expression of genes related to cell cycle, endoplasmic reticulum stress and apoptosis in peripheral blood mononuclear cells: a transcriptomic approach

BACKGROUND

Fish oil supplementation has been shown to alter gene expression of mononuclear cells both in vitro and in vivo. However, little is known about the total transcriptome profile in healthy subjects after intake of fish oil. We therefore investigated the gene expression profile in peripheral blood mononuclear cells (PBMCs) after intake of fish oil for 7 weeks using transcriptome analyses.

DESIGN

In a 7-week, double-blinded, randomized, controlled, parallel-group study, healthy subjects received 8 g day(-1) fish oil (1.6 g day(-1) eicosapentaenoic acid + docosahexaenoic acid) (n = 17) or 8 g day(-1) high oleic sunflower oil (n = 19). Microarray analyses of RNA isolated from PBMCs were performed at baseline and after 7 weeks of intervention.

RESULTS

Cell cycle, DNA packaging and chromosome organization are biological processes found to be upregulated after intake of fish oil compared to high oleic sunflower oil using a moderated t-test. In addition, gene set enrichment analysis identified several enriched gene sets after intake of fish oil. The genes contributing to the significantly different gene sets in the subjects given fish oil compared with the control group are involved in cell cycle, endoplasmic reticulum (ER) stress and apoptosis. Gene transcripts with common motifs for 35 known transcription factors including E2F, TP53 and ATF4 were upregulated after intake of fish oil.

CONCLUSION

We have shown that intake of fish oil for 7 weeks modulates gene expression in PBMCs of healthy subjects. The increased expression of genes related to cell cycle, ER stress and apoptosis suggests that intake of fish oil may modulate basic cellular processes involved in normal cellular function.

Predicting the virulence of MRSA from its genome sequence

Microbial virulence is a complex and often multifactorial phenotype, intricately linked to a pathogen’s evolutionary trajectory. Toxicity, the ability to destroy host cell membranes, and adhesion, the ability to adhere to human tissues, are the major virulence factors of many bacterial pathogens, including Staphylococcus aureus. Here, we assayed the toxicity and adhesiveness of 90 MRSA (methicillin resistant S. aureus) isolates and found that while there was remarkably little variation in adhesion, toxicity varied by over an order of magnitude between isolates, suggesting different evolutionary selection pressures acting on these two traits. We performed a genome-wide association study (GWAS) and identified a large number of loci, as well as a putative network of epistatically interacting loci, that significantly associated with toxicity. Despite this apparent complexity in toxicity regulation, a predictive model based on a set of significant single nucleotide polymorphisms (SNPs) and insertion and deletions events (indels) showed a high degree of accuracy in predicting an isolate’s toxicity solely from the genetic signature at these sites. Our results thus highlight the potential of using sequence data to determine clinically relevant parameters and have further implications for understanding the microbial virulence of this opportunistic pathogen.

GeneDB--an annotation database for pathogens

GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms.

Comparative whole genome sequence analysis of the carcinogenic bacterial model pathogen Helicobacter felis

The gram-negative bacterium Helicobacter felis naturally colonizes the gastric mucosa of dogs and cats. Due to its ability to persistently infect laboratory mice, H. felis has been used extensively to experimentally model gastric disorders induced in humans by H. pylori. We determined the 1.67 Mb genome sequence of H. felis using combined Solexa and 454 pyrosequencing, annotated the genome, and compared it with multiple previously published Helicobacter genomes. About 1,063 (63.6%) of the 1,671 genes identified in the H. felis genome have orthologues in H. pylori, its closest relative among the fully sequenced Helicobacter species. Many H. pylori virulence factors are shared by H. felis: these include the gamma-glutamyl transpeptidase GGT, the immunomodulator NapA, and the secreted enzymes collagenase and HtrA. Helicobacter felis lacks a Cag pathogenicity island and the vacuolating cytotoxin VacA but possesses a complete comB system conferring natural competence. Remarkable features of the H. felis genome include its paucity of transcriptional regulators and an extraordinary abundance of chemotaxis sensors and restriction/modification systems. Helicobacter felis possesses an episomally replicating 6.7-kb plasmid and harbors three chromosomal regions with deviating GC content. These putative horizontally acquired regions show homology and synteny with the recently isolated H. pylori plasmid pHPPC4 and homology to Campylobacter bacteriophage genes (transposases, structural, and lytic genes), respectively. In summary, the H. felis genome harbors a variety of putative mobile elements that are unique among Helicobacter species and may contribute to this pathogen’s carcinogenic properties.

A review of geometric transformations for nonrigid body registration

This paper provides a comprehensive and quantitative review of spatial transformations models for nonrigid image registration. It explains the theoretical foundation of the models and classifies them according to this basis. This results in two categories, physically based models described by partial differential equations of continuum mechanics (e.g., linear elasticity and fluid flow) and basis function expansions derived from interpolation and approximation theory (e.g., radial basis functions, B-splines and wavelets). Recent work on constraining the transformation so that it preserves the topology or is diffeomorphic is also described. The final section reviews some recent evaluation studies. The paper concludes by explaining under what conditions a particular transformation model is appropriate.