The Validation and Implications of Using Whole Genome Sequencing as a Replacement for Traditional Serotyping for a National Salmonella Reference Laboratory

Salmonella serotyping remains the gold-standard tool for the classification of Salmonella isolates and forms the basis of Canada’s national surveillance program for this priority foodborne pathogen. Public health officials have been increasingly looking toward whole genome sequencing (WGS) to provide a large set of data from which all the relevant information about an isolate can be mined. However, rigorous validation and careful consideration of potential implications in the replacement of traditional surveillance methodologies with WGS data analysis tools is needed. Two in silico tools for Salmonella serotyping have been developed, the Salmonella in silico Typing Resource (SISTR) and SeqSero, while seven gene MLST for serovar prediction can be adapted for in silico analysis. All three analysis methods were assessed and compared to traditional serotyping techniques using a set of 813 verified clinical and laboratory isolates, including 492 Canadian clinical isolates and 321 isolates of human and non-human sources. Successful results were obtained for 94.8, 88.2, and 88.3% of the isolates tested using SISTR, SeqSero, and MLST, respectively, indicating all would be suitable for maintaining historical records, surveillance systems, and communication structures currently in place and the choice of the platform used will ultimately depend on the users need. Results also pointed to the need to reframe serotyping in the genomic era as a test to understand the genes that are carried by an isolate, one which is not necessarily congruent with what is antigenically expressed. The adoption of WGS for serotyping will provide the simultaneous collection of information that can be used by multiple programs within the current surveillance paradigm; however, this does not negate the importance of the various programs or the role of serotyping going forward.

A Syst-OMICS Approach to Ensuring Food Safety and Reducing the Economic Burden of Salmonellosis

The Salmonella Syst-OMICS consortium is sequencing 4,500 Salmonella genomes and building an analysis pipeline for the study of Salmonella genome evolution, antibiotic resistance and virulence genes. Metadata, including phenotypic as well as genomic data, for isolates of the collection are provided through the Salmonella Foodborne Syst-OMICS database (SalFoS), at https://salfos.ibis.ulaval.ca/. Here, we present our strategy and the analysis of the first 3,377 genomes. Our data will be used to draw potential links between strains found in fresh produce, humans, animals and the environment. The ultimate goals are to understand how Salmonella evolves over time, improve the accuracy of diagnostic methods, develop control methods in the field, and identify prognostic markers for evidence-based decisions in epidemiology and surveillance.

Limited evidence of abnormal intra-colonic pressure profiles in diverticular disease - a systematic review

AIM

Abnormal colonic pressure profiles and high intraluminal pressures are postulated to contribute to the formation of sigmoid colon diverticulosis and the pathophysiology of diverticular disease. This study aimed to review evidence for abnormal colonic pressure profiles in diverticulosis.

METHOD

All published studies investigating colonic pressure in patients with diverticulosis were searched in three databases (Medline, Embase, Scopus). No language restrictions were applied. Any manometry studies in which patients with diverticulosis were compared with controls were included. The Newcastle-Ottawa Quality Assessment Scale (NOS) for case-control studies was used as a measure of risk of bias. A cut-off of five or more points on the NOS (fair quality in terms of risk of bias) was chosen for inclusion in the meta-analysis.

RESULTS

Ten studies (published 1962-2005) met the inclusion criteria. The studies followed a wide variety of protocols and all used low-resolution manometry (sensor spacing range 7.5-15 cm). Six studies compared intra-sigmoid pressure, with five of six showing higher pressure in diverticulosis vs controls, but only two reached statistical significance. A meta-analysis was not performed as only two studies were above the cut-off and these did not have comparable outcomes.

CONCLUSION

This systematic review of manometry data shows that evidence for abnormal pressure in the sigmoid colon in patients with diverticulosis is weak. Existing studies utilized inconsistent methodology, showed heterogeneous results and are of limited quality. Higher quality studies using modern manometric techniques and standardized reporting methods are needed to clarify the role of colonic pressure in diverticulosis.

Human Thiel-Embalmed Cadaveric Aortic Model with Perfusion for Endovascular Intervention Training and Medical Device Evaluation

Purpose

The purpose of this investigation was to evaluate human Thiel-embalmed cadavers with the addition of extracorporeal driven ante-grade pulsatile flow in the aorta as a model for simulation training in interventional techniques and endovascular device testing.

Materials and Methods

Three human cadavers embalmed according to the method of Thiel were selected. Extracorporeal pulsatile ante-grade flow of 2.5 L per min was delivered directly into the aorta of the cadavers via a surgically placed connection. During perfusion, aortic pressure and temperature were recorded and optimized for physiologically similar parameters. Pre- and post-procedure CT imaging was conducted to plan and follow up thoracic and abdominal endovascular aortic repair as it would be in a clinical scenario. Thoracic endovascular aortic repair (TEVAR) and endovascular abdominal repair (EVAR) procedures were conducted in simulation of a clinical case, under fluoroscopic guidance with a multidisciplinary team present.

Results

The Thiel cadaveric aortic perfusion model provided pulsatile ante-grade flow, with pressure and temperature, sufficient to conduct a realistic simulation of TEVAR and EVAR procedures. Fluoroscopic imaging provided guidance during the intervention. Pre- and post-procedure CT imaging facilitated planning and follow-up evaluation of the procedure.

Conclusion

The human Thiel-embalmed cadavers with the addition of extracorporeal flow within the aorta offer an anatomically appropriate, physiologically similar robust model to simulate aortic endovascular procedures, with potential applications in interventional radiology training and medical device testing as a pre-clinical model.

Electronic supplementary material

The online version of this article (doi:10.1007/s00270-017-1643-z) contains supplementary material, which is available to authorized users.

Abstract P2-10-02: The impact of intrinsic subtypes and molecular features on aromatase inhibitor induced reduction of proliferation marker of Ki67 in primary ER+ breast cancer: A POETIC study (CRUK/07/015)

Background

Neoadjuvant endocrine therapy (NAE) is often a good option for postmenopausal (PM) women with estrogen receptor positive (ER+) breast cancers(BC). Fall in Ki67 is widely accepted as valid for predicting favorable tumor response to NAE and improved outcome. We report our planned correlative study to investigate if intrinsic subtype impacts on Ki67 changes (ΔKi67) as measured by immunohistochemistry. We also explored the correlation of several ER+ BC relevant molecular features at baseline(B) with ΔKi67.

Patients and methods

POETIC is a phase III, randomized 2:1 study for 4486 PM patients with ER+ BC to determine whether peri-operative aromatase inhibitor (AI) followed by standard adjuvant therapy improves outcome compared with standard adjuvant therapy alone. The proliferation rate was estimated as percentage (%) of cancer cells staining for Ki67. Primary biological endpoint was defined as two-week (2wk) change in Ki67 (2wkΔKi67): ln[(2wk Ki67+0.1)/(B Ki67+0.1)]. Secondary endpoint: “responders”, was % change of Ki67 defined as (2wk Ki67 – B Ki67) *100/B Ki67. “Responder” was defined as follows: reduction <50% as poor (PR), 50-75% moderate and >75% as good responder (GR).

Human whole genome expression(GE) Illumina BeadChips were performed. Data was obtained from 137 paired samples from the treatment group(T) and 49 pairs from the control(C) group with GE data passing quality check and baseline Ki67≥5% to minimise the impact of extreme values based on proportional ΔKi67. Intrinsic subtype and risk of recurrence(ROR) groups were calculated using PAM50. GE scores from Oncotype Dx, MammaPrint, p53 mutation/wildtype(Troester 2006), ER+ early response (ERE)(Hatzis 2011), estrogen-regulated genes subtypes (Oh 2006) and markers for 23 different immune cell types(Bindea 2013) were calculated. Associations of GE scores to endpoints of response were determined by Spearman correlation and chi-square tests. Bonferroni correction was used to control error rate with p<0.0005 deemed significant.

Results

At B of the 137 paired T, 64% were Luminal A (LumA), 22% Luminal B (LumB), 9% as HER-2 enriched (HER2-E), 2% as Basal-like (BLBC) and 3% as Normal-like. Subtypes at B were associated with response, with LumA showing the biggest reduction of Ki67 (p=0.0001) and GR. All GE, except ERE, correlated significantly with 2wkΔKi67 and response: higher risk groups associated with lowest reduction rate. None of immune cell types correlated with 2wkΔKi67, except that tumors enriched with T-helper 1 cell type were associated with PR (p < 0.000001).

Comparing subtypes between time-points, 85% of LumB and 42% of HER2-E were assigned instead as LumA at 2wk regardless of response. Of the 15 ROR defined high-risk group, only 33% were assigned instead as low-risk at 2wk.

Conclusion

Both LumA and LumB are endocrine sensitive. A fall of Ki67 was observed in majority of cases. Most tumors estimated as high-risk by molecular profiling showed less response and most remained moderate or high risk of recurrence on endocrine therapy. Whether molecular profiling at 2wk after starting AI predicts for long-term outcome in PM women with ER+ better than at diagnosis will need to be determined.

Citation Format: Cheang MCU, Morden J, Gao Q, Parker J, López-Knowles E, Detre S, Hills M, Zabaglo L, Tomiczek M, Mallon E, Robertson J, Smith I, Bliss J, Dowsett M, On Behalf of the POETIC Trialists. The impact of intrinsic subtypes and molecular features on aromatase inhibitor induced reduction of proliferation marker of Ki67 in primary ER+ breast cancer: A POETIC study (CRUK/07/015) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-10-02.

Abstract P2-09-02: True effect of aromatase inhibitor (AI) treatment on global gene expression (expr) changes in postmenopausal ER+ breast cancer (BC) patients: A POETIC study (CRUK/07/015)

BACKGROUND Gene expression (expr) analyses are increasingly used for characterising the pharmacodynamic response of primary BC. This includes assessing ER+ BC's dependence on estrogen (E) by measuring gene expr changes after AI-treatment. However, differences in tissue sampling and other preanalytic procedures between samples taken at diagnosis (D) and surgery (S), may lead to systematic artifactual changes that are falsely ascribed to the intervention. To identify genes whose expr is truly affected by AI, we measured global gene expr changes from paired core-cut biopsies at D and S from patients in the POETIC presurgical window trial.

METHODS In POETIC, 4486 postmenopausal women with primary ER+ BC were randomised 2:1 to receive perioperative AI (2 weeks pre + 2 weeks post surgery, termed Tr) or no perioperative treatment (termed Con), allowing gene expr changes to be compared between Tr and Con. RNA was extracted from paired RNA-later stored core-cuts of 56 Con and 157 Tr patients and arrayed on Illumina whole genome expr BeadChips. Raw data was extracted, transformed, normalised and batch-corrected. Probes not detected (p>0.01) in >=25% of samples were discarded. Impact of AI on genes was evaluated based on difference of the expr mean changes (log2(S/D)) of the Tr and Con samples.

RESULTS In the Con group, expr of 73 genes significantly changed (FDR<5%); 70 of these changed by a similar magnitude in the Tr group, indicating their change was independent of AI therapy but would have been artifactually discovered as changed by AI in the absence on Con. The 8 genes most up-regulated in Tr were all among the 20 genes most up-regulated in Con: many were early-response or stress-associated genes. Three of the 8 most down-regulated in AI were the most down-regulated in Con: all were haemoglobin-related. Expr of some genes was changed in Con (eg MYC increase) but was unaffected in Tr. Such artifactual gene changes in Con tumors conceal true AI-induced changes that would not be detected in the absence of comparison with Con.

615 genes were down-regulated and 472 up-regulated in Tr but not Con. The majority of down-regulated genes were cell cycle or proliferation-associated or E-regulated, including ESR1, PDZK1, GREB1, HSPB1. Functional mapping showed changes in the regulation of cyclins and cyclin dependent kinases impacting on G1/S and G2/M. Of note, up-regulated genes included CDK6 (target for CDK4/6 inhibitors) and CCND2, involved in G1/S checkpoint regulation; SNAI2, TGFB3, TGFBR2, associated with tumour invasion and metastasis; and other genes involved in aryl hydrocarbon receptor, Glioblastoma Multiforme, HIPPO and p53 signalling.

CONCLUSION Expr of certain genes is altered by processes involved in presurgical window studies. In the absence of a Con group, these may be wrongly ascribed to an experimental intervention or wrongly considered as unaffected by the intervention (eg MYC in this study).

Down-regulation of E-responsive and proliferation genes was an expected response to AI but increased expr of genes such as SNAI2, CCND2 and CDK6 indicates immediate tumour re-wiring and provides mechanistic support for benefit from combination therapy with a CDK4/6 inhibitor.

Citation Format: Gao Q, López-Knowles E, Cheang MCU, Morden J, Martin L-A, Sidhu K, Evans D, Martins V, Dodson A, Skene A, Holcombe C, Mallon E, Abigail E, Bliss J, Robertson J, Smith I, Dowsett M. True effect of aromatase inhibitor (AI) treatment on global gene expression (expr) changes in postmenopausal ER+ breast cancer (BC) patients: A POETIC study (CRUK/07/015) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-09-02.

Sensitivity of simulated transcranial ultrasound fields to acoustic medium property maps

High intensity transcranial focused ultrasound is an FDA approved treatment for essential tremor, while low-intensity applications such as neurostimulation and opening the blood brain barrier are under active research. Simulations of transcranial ultrasound propagation are used both for focusing through the skull, and predicting intracranial fields. Maps of the skull acoustic properties are necessary for accurate simulations, and can be derived from medical images using a variety of methods. The skull maps range from segmented, homogeneous models, to fully heterogeneous models derived from medical image intensity. In the present work, the impact of uncertainties in the skull properties is examined using a model of transcranial propagation from a single element focused transducer. The impact of changes in bone layer geometry and the sound speed, density, and acoustic absorption values is quantified through a numerical sensitivity analysis. Sound speed is shown to be the most influential acoustic property, and must be defined with less than 4% error to obtain acceptable accuracy in simulated focus pressure, position, and volume. Changes in the skull thickness of as little as 0.1 mm can cause an error in peak intracranial pressure of greater than 5%, while smoothing with a 1 [Formula: see text] kernel to imitate the effect of obtaining skull maps from low resolution images causes an increase of over 50% in peak pressure. The numerical results are confirmed experimentally through comparison with sonications made through 3D printed and resin cast skull bone phantoms.

Neurotomy of the rectus femoris nerve: Short-term effectiveness for spastic stiff knee gait: Clinical assessment and quantitative gait analysis

BACKGROUND

Stiff knee gait is a troublesome gait disturbance related to spastic paresis, frequently associated with overactivity of the rectus femoris muscle in the swing phase of gait.

OBJECTIVE

The aim of this study was to assess the short-term effects of rectus femoris neurotomy for the treatment of spastic stiff-knee gait in patients with hemiparesis.

PATIENTS AND METHODS

An Intervention study (before-after trial) with an observational design was carried out in a university hospital. Seven ambulatory patients with hemiparesis of spinal or cerebral origin and spastic stiff-knee gait, which had previously been improved by botulinum toxin injections, were proposed a selective neurotomy of the rectus femoris muscle. A functional evaluation (Functional Ambulation Classification and maximal walking distance), clinical evaluation (spasticity - Ashworth scale and Duncan-Ely test, muscle strength - Medical Research Council scale), and quantitative gait analysis (spatiotemporal parameters, stiff knee gait-related kinematic and kinetic parameters, and dynamic electromyography of rectus femoris) were performed as outcome measures, before and 3 months after rectus femoris neurotomy.

RESULTS

Compared with preoperative values, there was a significant increase in maximal walking distance, gait speed, and stride length at 3 months. All kinematic parameters improved, and the average early swing phase knee extension moment decreased. The duration of the rectus femoris burst decreased post-op.

CONCLUSION

This study is the first to show that rectus femoris neurotomy helps to normalise muscle activity during gait, and results in improvements in kinetic, kinematic, and functional parameters in patients with spastic stiff knee gait.

Predictors of self-reported alcohol use and attitudes toward alcohol among 11-year-old British children with and without intellectual disability

BACKGROUND

Reducing harmful levels of alcohol consumption among children is an important public health concern internationally and in many high income countries. Little is known about levels and predictors of alcohol use among children with intellectual disability (ID).

METHOD

Secondary analysis of child self-report data at age 11 years collected in the UK's Millennium Cohort Study.

RESULTS

Children with ID were significantly more likely to: have used alcohol in the last 4 weeks; to have had five or more alcoholic drinks on one occasion; to have had five or more alcoholic drinks or been intoxicated on one occasion; to have more positive attitudes about the psychological and social benefits of drinking; and to have less negative attitudes about the social and physical costs of drinking. Potentially harmful levels of drinking (intoxication or 5+ alcoholic drinks on one occasion) among children with ID were associated with child smoking, having friends who use alcohol, reporting that drinking makes it easier to make friends, and reporting that drinking reduces worrying. Children with ID accounted for 9% of all children with potentially harmful levels of drinking.

CONCLUSION

Public health interventions to reduce potentially harmful drinking among children in general must recognise that children with ID are a potentially high risk group and ensure that interventions are appropriately adjusted to take account of their particular needs and situation. Future research in this area is needed to untangle the causal pathways between attitudes toward alcohol and alcohol use among children with ID and the extent to which levels of alcohol use and predictors of alcohol use may be moderated by severity of ID.

Assessing medication packaging and labelling appropriateness in Sri Lanka

Background

There is substantial evidence of poor dispensing practices with inadequate packaging and labelling of medicines, and limited advice on their usage in low and middle-income countries (LMICs). We examined the labelling and packaging of medicines identified during a survey of 1322 households in six regions of Sri Lanka between 2010 and 2013 conducted using the World Health Organization (WHO) methodology for household surveys. We compared medicines obtained from public and private sources and asked interviewees if they understood how to take the medicines.

Methods

Packaging was considered adequate when the primary package was an envelope or closable container holding only one medicine. Adequate labels were legible and included medicine name, dose and expiration date. Interviewers assessed whether respondents knew how to take the medicines.

Results

Of 1322 households, 1253 households (94.8%) had at least one medicine; 84% were classified as western medicines and 16% traditional medicines. Of 5756 western medicines identified, 82.1% were adequately packaged, 43.3% adequately labelled and 41.4% both adequately packaged and labelled. Participants stated that they understood the label and knew how to take 96% of the medicines. Private medicine sources had more adequately packaged medicines than public sources (87.7% vs 73.5%; OR 2.58, 95% CI 2.23, 2.99) and more adequately labelled medicines (52.2% vs 27.4%; OR 2.90, 95% CI 2.57, 3.26).

Conclusions

Inadequate packaging and labelling of medicines remain a concern in Sri Lanka. Commitment to Good Pharmacy Practices, investments in staff education and training and adequate dispensing resources (containers and labels), particularly in the public sector, are needed to address sub-optimal dispensing practices. Ageing populations with more chronic diseases requiring polypharmacy and complex medicine regimens increase the need for appropriately packaged and labelled medicines.

Electronic supplementary material

The online version of this article (doi:10.1186/s40545-016-0091-5) contains supplementary material, which is available to authorized users.