Genomic Surveillance of Foodborne Pathogens: Advances and Obstacles.

Context: The genomic surveillance of foodborne pathogens in the United States has grown exponentially in the past decade, grounded in a powerful combination of novel sequencing technologies, bioinformatic approaches, data-sharing networks, and metadata harmonization efforts. This practice report examines recent advances in genomic epidemiology as applied to food safety programs and delineates State, Tribal, Local, and Territorial infrastructure necessary for continued life-saving improvements in public health.

Program: National databases of foodborne pathogen genomes, along with data sharing and evaluation networks such as GenomeTrakr and PulseNet, have transformed how connections are made among isolates and how root causes of outbreaks are determined, allowing much more timely interventions to protect public health.

Examining the Severity and Progression of Illicitly Manufactured Fentanyl Withdrawal: A Quasi-Experimental Comparison.

Objective: Illicitly manufactured fentanyl has largely replaced heroin throughout the United States. Characteristics of fentanyl-specific withdrawal are not well understood compared to traditional opioid withdrawal. This study examines opioid withdrawal severity among 2 cohorts of study participants who underwent identical morphine stabilization procedures before and after fentanyl was introduced to the local drug market.

A comparison of visual and molecular methods for inferring biological communities in aquaculture enriched sediments - Impact assessment and cost-benefit analysis.

Nutrients introduced to the environment by finfish aquaculture pose environmental risks, which can be mitigated by robust environmental monitoring. Biological communities in soft sediments are good indicators of aquaculture derived environmental changes. Traditionally, monitoring programs have visually surveyed macrofauna communities.

The Concept of Treatment-Refractory Addiction: A Call to the Field.

Not all patients respond to effective and approved treatment interventions, and there has been growing recognition in the medical field of these "resistant" or refractory illnesses (eg, treatment-resistant depression, resistant hypertension). In the field of substance use disorders, there has not been an explicit acknowledgement of treatment-refractory addiction (TRA) despite substantial evidence that many patients do not respond to standard-of-care treatment interventions. This article provides a justification for TRA as a critically important condition to recognize and define.

Assessing the role of natural kelp forests in modifying seawater chemistry.

Climate change is causing widespread impacts on seawater pH through ocean acidification (OA). Kelp forests, in some locations can buffer the effects of OA through photosynthesis. However, the factors influencing this variation remain poorly understood.

A Comprehensive Guide to Quality Assessment and Data Submission for Genomic Surveillance of Enteric Pathogens.

This document outlines the steps necessary to assemble and submit the standard data package required for contributing to the global genomic surveillance of enteric pathogens. Although targeted to GenomeTrakr laboratories and collaborators, these protocols are broadly applicable for enteric pathogens collected for different purposes. There are five protocols included in this chapter: (1) quality control (QC) assessment for the genome sequence data, (2) validation for the contextual data, (3) data submission for the standard pathogen package or Pathogen Data Object Model (DOM) to the public repository, (4) viewing and querying data at NCBI, and (5) data curation for maintaining relevance of public data.

A one health approach for monitoring antimicrobial resistance: developing a national freshwater pilot effort.

Antimicrobial resistance (AMR) is a world-wide public health threat that is projected to lead to 10 million annual deaths globally by 2050. The AMR public health issue has led to the development of action plans to combat AMR, including improved antimicrobial stewardship, development of new antimicrobials, and advanced monitoring. The National Antimicrobial Resistance Monitoring System (NARMS) led by the United States (U.

Paired metagenomic and chemical evaluation of aflatoxin-contaminated dog kibble.

Introduction: Identification of chemical toxins from complex or highly processed foods can present 'needle in the haystack' challenges for chemists. Metagenomic data can be used to guide chemical toxicity evaluations by providing DNA-based description of the wholistic composition (eukaryotic, bacterial, protozoal, viral, and antimicrobial resistance) of foods suspected to harbor toxins, allergens, or pathogens. This type of information can focus chemistry-based diagnostics, improve hazard characterization and risk assessment, and address data gaps.

Examining NSDUH's Assessment of Fentanyl Use: A Comparison of Trends in Fentanyl Use and Fentanyl Overdose Deaths From 2015 to 2020.

Objective: The National Survey on Drug Use and Health (NSDUH), as the primary source of epidemiological substance use data in the United States, could illuminate trends in fentanyl use behaviors contributing to the opioid overdose crisis. We hypothesized that the trend in NSDUH prevalence of lifetime fentanyl injection would match the direction and magnitude of the trend in synthetic opioid overdose deaths.

Method: Using logistic regression, we modeled the 2015-2020 trend in synthetic opioid overdose deaths as a proportion of all deaths.

Virtual focus groups among individuals with use disorders: assessing feasibility and acceptability in an underserved clinical population.

Objective: There are substantial barriers to conducting research among individuals with stigmatized and complicated health conditions like substance use disorders. These barriers slow progress when developing, refining, and assessing interventions to better treat underserved populations. Virtual focus groups are an innovative method for collecting data from individuals via a discreet and accessible platform which can inform novel as well as existing treatment approaches.

Establishing a research agenda for the study and assessment of opioid withdrawal.

The opioid crisis is an international public health concern. Treatments for opioid use disorder centre largely on the management of opioid withdrawal, an aversive collection of signs and symptoms that contribute to opioid use disorder. Whereas in the past 50 years more than 90 medications have been developed for depression, only five medications have been developed for opioid use disorder during this period.

The spread of pESI-mediated extended-spectrum cephalosporin resistance in Salmonella serovars-Infantis, Senftenberg, and Alachua isolated from food animal sources in the United States.

The goal of this study is to investigate the origin, prevalence, and evolution of the pESI megaplasmid in Salmonella isolated from animals, foods, and humans. We queried 510,097 Salmonella genomes under the National Center for Biotechnology Information (NCBI) Pathogen Detection (PD) database for the presence of potential sequences containing the pESI plasmid in animal, food, and environmental sources. The presence of the pESI megaplasmid was confirmed by using seven plasmid-specific markers (rdA, pilL, SogS, TrbA, ipf, ipr2 and IncFIB(pN55391)).

Complexity-functioning relationships differ across different environmental conditions.

Habitat complexity is widely considered an important determinant of biodiversity, and enhancing complexity can play a key role in restoring degraded habitats. However, the effects of habitat complexity on ecosystem functioning - as opposed to biodiversity and community structure - are relatively poorly understood for artificial habitats, which dominate many coastlines. With Greening of Grey Infrastructure (GGI) approaches, or eco-engineering, increasingly being applied around the globe, it is important to understand the effects that modifying habitat complexity has on both biodiversity and ecological functioning in these highly modified habitats.

Suvorexant alters dynamics of the sleep-electroencephalography-power spectrum and depressive-symptom trajectories during inpatient opioid withdrawal.

Study Objectives: Opioid withdrawal is an aversive experience that often exacerbates depressive symptoms and poor sleep. The aims of the present study were to examine the effects of suvorexant on oscillatory sleep-electroencephalography (EEG) band power during medically managed opioid withdrawal, and to examine their association with withdrawal severity and depressive symptoms.

Methods: Participants with opioid use disorder (N = 38: age-range:21-63, 87% male, 45% white) underwent an 11-day buprenorphine taper, in which they were randomly assigned to suvorexant (20 mg [n = 14] or 40 mg [n = 12]), or placebo [n = 12], while ambulatory sleep-EEG data was collected.

Polymorphisms in the A118G SNP of the OPRM1 gene produce different experiences of opioids: A human laboratory phenotype-genotype assessment.

Allelic variations in the A118G SNP of the OPRM1 gene change opioid signaling; however, evaluations of how allelic differences may influence opioid effects are lacking. This human laboratory paradigm examined whether the AA versus AG/GG genotypes determined opioid response profiles. Individuals with limited opioid exposure (N = 100) completed a five-day within-subject, double-blind, placebo-controlled, residential study.

Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact.

Here, we examine surface waters as a modality to better understand baseline antimicrobial resistance (AMR) across the environment to supplement existing AMR monitoring in pathogens associated with humans, foods, and animals. Data from metagenomic and quasimetagenomic (shotgun sequenced enrichments) are used to describe AMR in Maryland surface waters from high and low human impact classifications.

Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting.

Here, we describe the fecal microbiome of laboratory beagles in a non-invasive experiment designed to contrast versus bioequivalence in response to antiparasitic drug administration. The experiment provided a unique opportunity to evaluate metagenomic profiles of canine feces before and after anti-parasitic drug exposure.

Genomic analysis of azithromycin-resistant from food animals at slaughter and processing, and retail meats, 2011-2021, United States.

Macrolides of different ring sizes are critically important antimicrobials for human medicine and veterinary medicine, though the widely used 15-membered ring azithromycin in humans is not approved for use in veterinary medicine. We document here the emergence of azithromycin-resistant among the NARMS culture collections between 2011 and 2021 in food animals and retail meats, some with co-resistance to ceftriaxone or decreased susceptibility to ciprofloxacin. We also provide insights into the underlying genetic mechanisms and genomic contexts, including the first report of a novel combination of azithromycin resistance determinants and the characterization of multidrug-resistant plasmids.

Increases in primary opioid use disorder diagnoses co-occurring with anxiety or depressive disorder diagnoses in mental health treatment in the United States, 2015-2019.

Background: Opioid use disorders (OUDs) often co-occur with anxiety and depressive disorders. While the proportion of mental health (MH) treatment facilities providing substance use treatment has increased, the proportion of these facilities able to simultaneously treat MH and substance use decreased. This warrants investigation into the integrated treatment needs of persons with a primary OUD diagnosis treated in MH treatment facilities.