Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States

ABSTRACT

This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety.

HIGHLIGHTS

Oh what a tangled web we weave when first we practice to deceive…

‘Oh what a tangled web we weave when first we practice to deceive’. Marmion, Sir Walter Scott 1808. Conflict is unpleasant, it is aversive, we tend to avoid it. Yet inevitably tension between individuals or between individuals and society is inevitable as the wants of one collide with the purpose of the other. Most of these tensions resolved peacefully but a societal level aggression can sometimes spill out. In the hinterlands between individuals and larger groups these can play out more safely through the courts or sometimes the avoidance of conflict can be the only tactic that the individual can use. As doctors we are used to sing medical problems with patients have true disease believe they have two disease and want to get well-the standard social model of medicine. But sometimes this plays out differently there are those who may fabricate symptoms to avoid punishment or for reward: malingering. There are those who believe they have a disease but the distress is disproportionate to any possible recognised component; somatic symptom disorder. There are those whose anxiety about whether they have a disease or not is paralysing and perhaps most distressing for all of the groups who self-harm or malinger with authentic illness or disease. In this talk Dr Wise will, using case examples, look at a couple of the tools that exist to assist psychiatrists in piloting a pathway through the stormy waters of abnormal illness in litigation.

Diagnostic dilemma’s in the new world of ICD-11 personality disorders

Personality disorders have ever been a troublesome group. From the early 90’s ICD 10 tidied up the group. DSM-IV, IV-TR, aand then DSM 5, changed the style but not substance, leaving clinicians to grapple with thorny questions of multiple diagnoses, treatment and prognosis. International views on the utility of the diagnosis often depended upon the institution or the funding mechanism. Were fears of exclusion and stigma dominated or where there was no treatment, there was under-diagnosis, such as in the United Kingdom and the Republic of Ireland. Where a label was a ticket of entry to treatment and funding, diagnostic generosity prevailed, such as in Australia, New Zealand and the United States. Gender discrepancies disappeared with structured interviews, and interest grew in the category which seem to only include the most severe forms. For many years the DSM taskforce tried to shift the construct but shied away from the cliff edge; a bold new initiative did not materialise. It was left to the ICD-11 to generate a much more adventurous and positive view of how characterological traits shift under pressure, moving from something that may at first have helped patients to ‘survive’ to something that became maladaptive and harmful. With a court tested case Dr Wise will demonstrate the differences between ICD-10 and ICD-11 highlighting the more important differences: onset, course and severity descriptors. PD’s are no longer lifelong impairments. Prepare for ‘The shock of the new’!

Detecting national human enteric disease outbreaks linked to animal contact in the United States of America

Enteric pathogens, such as non-typhoidal Salmonella, Campylobacter and Escherichia coli, can reside in the intestinal tract of many animals, including livestock, companion animals, small mammals and reptiles. Often, these animals can appear healthy; nonetheless, humans can become infected after direct or indirect contact, resulting in a substantial illness burden. An estimated 14% of the 3.2 million illnesses that occur in the United States of America (USA) each year from such enteric pathogens are attributable to animal contact. Surveillance for enteric pathogens in the USA includes the compilation and interpretation of both laboratory and epidemiologic data. However, the authors feel that a collaborative, multisectoral and transdisciplinary - or One Health - approach is needed for data collection and analysis, at every level. In addition, they suggest that the future of enteric illness surveillance lies in the development of improved technologies for pathogen detection and characterisation, such as genomic sequencing and metagenomics. In particular, using whole-genome sequencing to compare genetic sequences of enteric pathogens from humans, food, animals and the environment, can help to predict antimicrobial resistance among these pathogens, determine their genetic relatedness and identify outbreaks linked to a common source. In this paper, the authors describe three recent, multi-state human enteric illness outbreaks linked to animal contact in the USA and discuss how integrated disease surveillance was essential to outbreak detection and response. Additional datasharing between public health and animal health laboratories and epidemiologists at the local, national, regional and international level may help to improve surveillance for emerging animal and human health threats and lead to new opportunities for prevention.

Artificial neural networks improve early outcome prediction and risk classification in out-of-hospital cardiac arrest patients admitted to intensive care

Background

Pre-hospital circumstances, cardiac arrest characteristics, comorbidities and clinical status on admission are strongly associated with outcome after out-of-hospital cardiac arrest (OHCA). Early prediction of outcome may inform prognosis, tailor therapy and help in interpreting the intervention effect in heterogenous clinical trials. This study aimed to create a model for early prediction of outcome by artificial neural networks (ANN) and use this model to investigate intervention effects on classes of illness severity in cardiac arrest patients treated with targeted temperature management (TTM).

Methods

Using the cohort of the TTM trial, we performed a post hoc analysis of 932 unconscious patients from 36 centres with OHCA of a presumed cardiac cause. The patient outcome was the functional outcome, including survival at 180 days follow-up using a dichotomised Cerebral Performance Category (CPC) scale with good functional outcome defined as CPC 1–2 and poor functional outcome defined as CPC 3–5. Outcome prediction and severity class assignment were performed using a supervised machine learning model based on ANN.

Results

The outcome was predicted with an area under the receiver operating characteristic curve (AUC) of 0.891 using 54 clinical variables available on admission to hospital, categorised as background, pre-hospital and admission data. Corresponding models using background, pre-hospital or admission variables separately had inferior prediction performance. When comparing the ANN model with a logistic regression-based model on the same cohort, the ANN model performed significantly better (p = 0.029). A simplified ANN model showed promising performance with an AUC above 0.852 when using three variables only: age, time to ROSC and first monitored rhythm. The ANN-stratified analyses showed similar intervention effect of TTM to 33 °C or 36 °C in predefined classes with different risk of a poor outcome.

Conclusion

A supervised machine learning model using ANN predicted neurological recovery, including survival excellently, and outperformed a conventional model based on logistic regression. Among the data available at the time of hospitalisation, factors related to the pre-hospital setting carried most information. ANN may be used to stratify a heterogenous trial population in risk classes and help determine intervention effects across subgroups.

0408 Myths About Infant, Child, and Adolescent Sleep: Addressing False Beliefs That Hinder Sleep Health During These Crucial Developmental Stages

Introduction

Sleep is vital for healthy development from infancy through adolescence. Despite its importance, false beliefs that conflict with scientific evidence (myths) may be common among caregivers and impair sleep health during these crucial stages.

Methods

Researchers compiled a list of potential myth statements using internet searches of popular press and scientific literature. We utilized a Delphi process with experts (n=12) from the fields of pediatric, sleep, and circadian research and clinical practice. Selection and refinement of myths by sleep experts proceeded in three phases, including: focus groups (Phase 1); email-based feedback to edit, add, or remove myths (Phase 2); and closed-ended questionnaires (Phase 3) where experts rated myths on two dimensions: (1) falseness and (2) public health significance using 5-point Likert scale: 1 (“not at all”) to 5 (“extremely false/important”).

Results

Thirty-two sleep myths were identified across three developmental categories: infant (14 myths), child (6 myths), and adolescent (12 myths). Mean expert ratings illuminated the most pressing myths in each developmental category: infant sleep (“Sleep training causes psychological harm, including reduced parent-child attachment:” falseness =4.7, s.d.=0.7; public health significance=4.0, s.d.=1.1); child sleep (“Heavy, loud snoring for my child means he’s sleeping deeply:” falseness=4.8, s.d.=0.6; public health significance=4.7, s.d.=0.7), and teenager sleep (“Falling asleep in class means your teenager is lazy and not motivated:” falseness=4.8, s.d.=0.5; public health significance=4.3, s.d.=0.8).

Conclusion

The current study identified commonly-held myths about infant, child, and adolescent sleep that are not supported by (or worse, counter to) scientific evidence. If unchecked, these myths may hinder sleep at a critical developmental stage. Future research may include public health education to correct myths and promote healthy sleep among infants, children, and teenagers.

Support

5T32HL007901

Copeptin as a marker of outcome after cardiac arrest: a sub-study of the TTM trial

Background

Arginine vasopressin has complex actions in critically ill patients, involving vasoregulatory status, plasma volume, and cortisol levels. Copeptin, a surrogate marker for arginine vasopressin, has shown promising prognostic features in small observational studies and is used clinically for early rule out of acute coronary syndrome. The objective of this study was to explore the association between early measurements of copeptin, circulatory status, and short-term survival after out-of-hospital cardiac arrest.

Methods

Serial blood samples were collected at 24, 48, and 72 h as part of the target temperature management at 33 °C versus 36 °C after cardiac arrest trial, an international multicenter randomized trial where unconscious survivors after out-of-hospital cardiac arrest were allocated to an intervention of 33 or 36 °C for 24 h. Primary outcome was 30-day survival with secondary endpoints circulatory cause of death and cardiovascular deterioration composite; in addition, we examined the correlation with extended the cardiovascular sequential organ failure assessment (eCvSOFA) score.

Results

Six hundred ninety patients were included in the analyses, of whom 203 (30.3%) developed cardiovascular deterioration within 24 h, and 273 (39.6%) died within 30 days. Copeptin measured at 24 h was found to be independently associated with 30-day survival, hazard ratio 1.17 [1.06–1.28], p = 0.001; circulatory cause of death, odds ratio 1.03 [1.01–1.04], p = 0.001; and cardiovascular deterioration composite, odds ratio of 1.05 [1.02–1.08], p < 0.001. Copeptin at 24 h was correlated with eCvSOFA score with rho 0.19 [0.12–0.27], p < 0.001.

Conclusion

Copeptin is an independent marker of severity of the post cardiac arrest syndrome, partially related to circulatory failure.

Trial registration

Clinical Trials, NCT01020916. Registered November 26, 2009.

Outbreak Characteristics and Epidemic Curves for Multistate Outbreaks of Salmonella Infections Associated with Produce: United States, 2009-2015

Produce is recognized as a source of Salmonella-related foodborne outbreaks in the United States. Identifying produce as a source of foodborne outbreaks is challenging given short product shelf lives and durations of many produce-associated outbreaks. Investigators consider produce a plausible source when illnesses occur over a short time period and disproportionately affect middle-aged or female individuals. We reviewed characteristics of past Salmonella produce outbreaks and their consistency with principles used by epidemiologists when generating hypotheses about an outbreak source. We queried the Foodborne Disease Outbreak Surveillance System for multistate, produce-associated Salmonella outbreaks reported to the Centers for Disease Control and Prevention from 2009 to 2015. All produce-associated outbreaks were classified as fruit outbreaks or vegetable outbreaks using an established classification scheme. We then compared fruit and vegetable outbreaks by characteristics of size, gender, age, age groups, geographic spread, duration, and velocity measures using Wilcoxon rank-sum tests. Epidemic curves were created to display visual representations of outbreak duration and velocity. We identified 14 fruit outbreaks and 24 vegetable outbreaks. The median number of illnesses for all produce-associated outbreaks was 30 and a high median percentage of illnesses were in females (61.9%). Median age was 34 years, with a median of 53.2% of illnesses affecting the 18-59 age group. For all outbreaks, median duration was 77 d and median time to the 50th percentile of illnesses was 32.5 d. Fruit and vegetable outbreaks differed only in the age groups affected. We used outbreak data to verify common indicators of produce-associated Salmonella outbreaks. Outbreaks affected females and middle-aged individuals more commonly, while fruit and vegetable outbreaks impacted different age groups. Although median outbreak duration was less than 12 weeks for both fruit and vegetable outbreaks, there was considerable variation, decreasing its utility as an indicator of produce as a source of the outbreak.

A radio ridge connecting two galaxy clusters in a filament of the cosmic web

Galaxy clusters are the most massive gravitationally bound structures in the Universe. They grow by accreting smaller structures in a merging process that produces shocks and turbulence in the intracluster gas. We observed a ridge of radio emission connecting the merging galaxy clusters Abell 0399 and Abell 0401 with the Low-Frequency Array (LOFAR) telescope network at 140 megahertz. This emission requires a population of relativistic electrons and a magnetic field located in a filament between the two galaxy clusters. We performed simulations to show that a volume-filling distribution of weak shocks may reaccelerate a preexisting population of relativistic particles, producing emission at radio wavelengths that illuminates the magnetic ridge.

Lactate, lactate clearance and outcome after cardiac arrest: A post-hoc analysis of the TTM-Trial

BACKGROUND

Admission lactate and lactate clearance are implemented for risk stratification in sepsis and trauma. In out-of-hospital cardiac arrest, results regarding outcome and lactate are conflicting.

METHODS

This is a post-hoc analysis of the Target Temperature Management trial in which 950 unconscious patents after out-of-hospital cardiac arrest were randomized to a temperature intervention of 33°C or 36°C. Serial lactate samples during the first 36 hours were collected. Admission lactate, 12-hour lactate, and the clearance of lactate within 12 hours after admission were analyzed and the association with 30-day mortality assessed.

RESULTS

Samples from 877 patients were analyzed. In univariate logistic regression analysis, the odds ratio for death by day 30 for each mmol/L was 1.12 (1.08-1.16) for admission lactate, P < .01, 1.21 (1.12-1.31) for 12-hour lactate, P < .01, and 1.003 (1.00-1.01) for each percentage point increase in 12-hour lactate clearance, P = .03. Only admission lactate and 12-hour lactate levels remained significant after adjusting for known predictors of outcome. The area under the receiver operating characteristic curve was 0.65 (0.61-0.69), P < .001, 0.61 (0.57-0.65), P < .001, and 0.53 (0.49-0.57), P = .15 for admission lactate, 12-hour lactate, and 12-hour lactate clearance, respectively.

CONCLUSIONS

Admission lactate and 12-hour lactate values were independently associated with 30-day mortality after out-of-hospital cardiac arrest while 12-hour lactate clearance was not. The clinical value of lactate as the sole predictor of outcome after out-of-hospital cardiac arrest is, however, limited.

Chemoradiotherapy for squamous cell anal carcinoma: a review of prognostic factors

AIM

Previous literature has sought prognostic factors for the survival of anal cancer patients. The present study aimed to determine prognostic factors for local disease recurrence, distant metastasis and survival for patients treated with radical chemoradiotherapy (CRT) at the Rosemere Cancer Centre, Preston, UK.

METHOD

Patients treated with CRT for nonmetastatic squamous cell anal cancer between September 2000 and January 2013 were studied. Kaplan-Meier and Cox regression analysis assessed the prognostic value of age, sex, tumour size, the proportion of the anal canal circumference involved (ACCI), nodal disease, tumour location and pretreatment haemoglobin.

RESULTS

One hundred and 48 patients with a mean age of 63 years were studied, of whom 15% suffered local disease recurrence and 10% developed distant metastasis. The 5-year overall and cancer-specific survival rates were 84% and 86%, respectively. Predictors of local recurrence were tumour size >5 cm and over two-thirds ACCI (P < 0.01). Predictors of distant metastasis and poor survival were tumour size >5 cm (P < 0.01), node positive disease on imaging (P < 0.05), over two-thirds ACCI (P < 0.01) and a pretreatment haemoglobin level below 130 g/l (P < 0.05). Multivariate analysis found large tumour size to be the most significant factor for local recurrence (P = 0.002) and survival (P = 0.02) whilst over two-thirds ACCI was most predictive of distant metastasis (P < 0.001). Age, gender, palpable lymph nodes and tumour location were not of prognostic value for local disease recurrence, distant metastasis or survival.

CONCLUSION

Tumour size, nodal disease, over two-thirds ACCI and low pretreatment haemoglobin confer poorer prognostic and survival outcomes. Use of intensity-modulated radiation therapy may allow greater radiation doses to be given for locally advanced tumours, thus improving local control and survival and reducing morbidity.

New methods to constrain the radio transient rate: results from a survey of four fields with LOFAR

We report on the results of a search for radio transients between 115 and 190 MHz with the LOw-Frequency ARray (LOFAR). Four fields have been monitored with cadences between 15 min and several months. A total of 151 images were obtained, giving a total survey area of 2275 deg². We analysed our data using standard LOFAR tools and searched for radio transients using the LOFAR Transients Pipeline. No credible radio transient candidate has been detected; however, we are able to set upper limits on the surface density of radio transient sources at low radio frequencies. We also show that low-frequency radio surveys are more sensitive to steep-spectrum coherent transient sources than GHz radio surveys. We used two new statistical methods to determine the upper limits on the transient surface density. One is free of assumptions on the flux distribution of the sources, while the other assumes a power-law distribution in flux and sets more stringent constraints on the transient surface density. Both of these methods provide better constraints than the approach used in previous works. The best value for the upper limit we can set for the transient surface density, using the method assuming a power-law flux distribution, is 1.3 × 10^-3 deg^-2 for transients brighter than 0.3 Jy with a time-scale of 15 min, at a frequency of 150 MHz. We also calculated for the first time upper limits for the transient surface density for transients of different time-scales. We find that the results can differ by orders of magnitude from previously reported, simplified estimates.

Assessment for possible healthcare-associated transmission of a new variant influenza virus--Pennsylvania, August 2011

In August 2011, one of the earliest cases of influenza A(H3N2) variant [A(H3N2)v] virus infection was hospitalized with severe illness. To investigate the potential for healthcare-associated transmission of influenza A(H3N2)v, we evaluated both healthcare providers and patient contacts of the case. We found that healthcare-associated transmission was unlikely.

MESAFace, a graphical interface to analyze the MESA output

MESA (Modules for Experiments in Stellar Astrophysics) has become very popular among astrophysicists as a powerful and reliable code to simulate stellar evolution. Analyzing the output data thoroughly may, however, present some challenges and be rather time-consuming. Here we describe MESAFace, a graphical and dynamical interface which provides an intuitive, efficient and quick way to analyze the MESA output.

NATURE OF PROBLEM

Find a way to quickly and thoroughly analyze the output of a MESA run, including all the profiles, and have an efficient method to produce graphical representations of the data.

SOLUTION METHOD

We created two scripts (to be run consecutively). The first one downloads all the data from a MESA run and organizes the profiles in order of age. All the files are saved as tables or arrays of tables which can then be accessed very quickly by Mathematica. The second script uses the Manipulate function to create a graphical interface which allows the user to choose what to plot from a set of menus and buttons. The information shown is updated in real time. The user can access very quickly all the data from the run under examination and visualize it with plots and tables.

UNUSUAL FEATURES

Moving the slides in certain regions may cause an error message. This happens when Mathematica is asked to read nonexistent data. The error message, however, disappears when the slides are moved back. This issue does not preclude the good functioning of the interface.

ADDITIONAL COMMENTS

The program uses the dynamical capabilities of Mathematica. When the program is opened, Mathematica prompts the user to "Enable Dynamics". It is necessary to accept before proceeding.

RUNNING TIME

Depends on the size of the data downloaded, on where the data are stored (hard-drive or web), and on the speed of the computer or network connection. In general, downloading the data may take from a minute to several minutes. Loading directly from the web is slower. For example, downloading a 200MB data folder (a total of 102 files) with a dual-core Intel laptop, P8700, 2 GB of RAM, at 2.53 GHz took about a minute from the hard-drive and about 23 minutes from the web (with a basic home wireless connection).

A psychotherapy program for soldiers dependents: The effect on recall rates. “They are not going for three weeks and the fighting has already begun!”

Introduction

Deployment to conflict areas poses problems for service families. These stressors pose a high cost from increased rates of marital/family break-up and the impact on operational effectiveness, through early recall from combat zones. Soldiers look forward to a mission whilst partners are more ambivalent. The time before deployment is hard on those who stay behind, who experience high levels of anxiety. Those about to be deployed feel guilty, and have to manage their own anxieties about what the mission will bring - hard work, excitement and danger. Most do not talk about this to their partners, who in turn have to manage their own inner turmoil and worst case ‘fantasies’.

Aims

The project grew from concerns about the welfare of families of deployed army personnel.

Objectives

The project aimed to help them develop a greater capacity to manage, contain and function with these worries. The program provided psychodynamic psychoanalytic practices to a previously neglected group that was not wholly army, but is essential to its well-being.

Methods

The program gave the families a greater understanding of the emotional difficulties faced by their partners before, during and after deployment and lessened the stress in their relationships; strengthening their own and their partners’ sense of self, resilience, and the marital bond.

Results

Usually 3–5% of a unit would be recalled from combat operations, over the duration of a tour, this was reduced to 1%.

Conclusion

A psychotherapy programme for the families of soldiers reduces attrition rates.

Thermal plasma technology for the treatment of wastes: a critical review

This review describes the current status of waste treatment using thermal plasma technology. A comprehensive analysis of the available scientific and technical literature on waste plasma treatment is presented, including the treatment of a variety of hazardous wastes, such as residues from municipal solid waste incineration, slag and dust from steel production, asbestos-containing wastes, health care wastes and organic liquid wastes. The principles of thermal plasma generation and the technologies available are outlined, together with potential applications for plasma vitrified products. There have been continued advances in the application of plasma technology for waste treatment, and this is now a viable alternative to other potential treatment/disposal options. Regulatory, economic and socio-political drivers are promoting adoption of advanced thermal conversion techniques such as thermal plasma technology and these are expected to become increasingly commercially viable in the future.

[Community-based health promotion--a challenge for the evaluation]

PURPOSE

Community-based health promotion (CBHP) aims at mobilising citizens for health-related issues in their environment, and at implementing health-promoting projects on the community level. Whereas recent political decisions support this approach, scientific studies dealing with theories and consequences of CBHP are scarce in Germany. Evaluation of CBHP could help identify (in)effective factors and elements of community programmes and thus improve future planning. In Germany, however, there is a deficit in systematic concepts and recommendations for the evaluation of CBHP. This work outlines basic ideas and core principles of CBHP and deduces implications for the assessment of health-promoting community projects.

METHODS

Based on different international models and studies and on discussions with health promotion professionals, we developed a framework for the evaluation of CBHP.

RESULTS

The proposed framework includes a guideline for CBHP programme planning. Its strategic and operational criteria can serve as a basis for a strategy evaluation. In terms of process evaluation, indicators for the dimensions (1) programme implementation and service delivery, (2) capacity building, and (3) reach of and acceptability in the target group were developed. In addition, we present different areas of OUTCOME EVALUATION; it is advisable to distinguish between measurement on the individual and on the community level. The framework further proposes strategies for the evaluation of the core principles empowerment and participation.

CONCLUSION

The presented framework can serve as a basis for the development of flexible and individual instruments for the evaluation of CBHP, which should not ignore the perspective of the citizens, or complex aspects like changes on the community level. Some aspects, e.g., the potential evaluation of further targets of CBHP (improvement of quality of life, reduction of social and health inequalities), the responsibility of evaluation or the effects of financial constraints, are important questions to be addressed in the future.