Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021.

BACKGROUND: Monitoring the emergence and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is an important public health objective. We investigated how the Gamma variant was established in New York City (NYC) in early 2021 in the presence of travel restrictions that aimed to prevent viral spread from Brazil, the country where the variant was first identified. METHODS: We performed phylogeographic analysis on 15 967 Gamma sequences sampled between 10 March and 1 May 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC. RESULTS: We identified 16 phylogenetically distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes); most of them were introduced from Florida and Illinois and only 1 directly from Brazil. By the time the first Gamma case was reported by genomic surveillance in NYC on 10 March, the majority (57%) of circulating Gamma lineages had already been established in the city for at least 2 weeks. CONCLUSIONS: Although travel from Brazil to the United States was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.

Genome-Based Prediction of Bacterial Antibiotic Resistance.

Clinical microbiology has long relied on growing bacteria in culture to determine antimicrobial susceptibility profiles, but the use of whole-genome sequencing for antibiotic susceptibility testing (WGS-AST) is now a powerful alternative. This review discusses the technologies that made this possible and presents results from recent studies to predict resistance based on genome sequences. We examine differences between calling antibiotic resistance profiles by the simple presence or absence of previously known genes and single-nucleotide polymorphisms (SNPs) against approaches that deploy machine learning and statistical models. Often, the limitations to genome-based prediction arise from limitations of accuracy of culture-based AST in addition to an incomplete knowledge of the genetic basis of resistance. However, we need to maintain phenotypic testing even as genome-based prediction becomes more widespread to ensure that the results do not diverge over time. We argue that standardization of WGS-AST by challenge with consistently phenotyped strain sets of defined genetic diversity is necessary to compare the efficacy of methods of prediction of antibiotic resistance based on genome sequences.

Experiences of baccalaureate nursing students in preceptorship during the COVID-19 pandemic: a systematic review protocol.

OBJECTIVE: The objective of this review is to appraise and synthesize current evidence of the clinical experiences of baccalaureate nursing students in preceptorship during the COVID-19 pandemic. INTRODUCTION: Nursing education programs support quality clinical practice learning experiences, which are essential for preparing students for both the current and future workforce. The COVID-19 pandemic has drastically changed the health care system and, previous estimates of the global shortage of nurses have now almost doubled. Understanding nursing students' clinical experiences during the pandemic can assist with identifying the needs of the future workforce. Nursing students complete the final practicum, also known as the last clinical, internship, or preceptorship, before they are eligible to apply for licensure. This review seeks to explore these pre-transitional, unprecedented preceptorship experiences during COVID-19 to better understand how to prepare pre-licensure nurses for the altered workforce. INCLUSION CRITERIA: This review will include qualitative studies that address the clinical experiences of undergraduate nursing students in preceptorship during the COVID-19 pandemic from 2020 until the present. METHODS: The databases to be searched will include CINAHL, MEDLINE, ERIC, Google Scholar, and Embase. Reference lists of included studies will be reviewed to identify additional studies. Gray literature will be searched for via ProQuest Dissertations and Theses, Google, and GreyNet International. Unpublished studies will be searched for on websites, including those of national associations of nursing. Study selection, critical appraisal, data extraction, and data synthesis will be performed independently by 2 reviewers. The findings will be collated using meta-aggregation to produce comprehensive synthesized findings and a ConQual Summary of Findings. REVIEW REGISTRATION: PROSPERO CRD42022328303.

SARS-CoV-2 lineage assignments using phylogenetic placement/UShER are superior to pangoLEARN machine-learning method.

With the rapid spread and evolution of SARS-CoV-2, the ability to monitor its transmission and distinguish among viral lineages is critical for pandemic response efforts. The most commonly used software for the lineage assignment of newly isolated SARS-CoV-2 genomes is pangolin, which offers two methods of assignment, pangoLEARN and pUShER. PangoLEARN rapidly assigns lineages using a machine-learning algorithm, while pUShER performs a phylogenetic placement to identify the lineage corresponding to a newly sequenced genome. In a preliminary study, we observed that pangoLEARN (decision tree model), while substantially faster than pUShER, offered less consistency across different versions of pangolin v3. Here, we expand upon this analysis to include v3 and v4 of pangolin, which moved the default algorithm for lineage assignment from pangoLEARN in v3 to pUShER in v4, and perform a thorough analysis confirming that pUShER is not only more stable across versions but also more accurate. Our findings suggest that future lineage assignment algorithms for various pathogens should consider the value of phylogenetic placement.

Severe Mpox Among People With Advanced Human Immunodeficiency Virus Receiving Prolonged Tecovirimat in New York City.

Severe mpox has been observed in people with advanced human immunodeficiency virus (HIV). We describe clinical outcomes of 13 patients with advanced HIV (CD4 <200 cells/µL), severe mpox, and multiorgan involvement. Despite extended tecovirimat courses and additional agents, including vaccinia immune globulin, cidofovir, and brincidofovir, this group experienced prolonged hospitalizations and high mortality.

New methods for estimating the total wing area of birds.

Dispersal is a fundamental process in evolution and ecology. Due to the predominant role of flight in bird movement, their dispersal capabilities can be estimated from their flight morphology. Most predictors of flight efficiency require an estimate of the total wing area, but the existing methods for estimating wing area are multi-stepped and prone to compounding error. Here, we validated a new method for estimating the total wing area that requires only the measurement of the wingspan plus two measurements from the folded wings of study skin specimens: wing length and wing width. We demonstrate that the new folded-wing method estimates total wing area with high precision across a variety of avian groups and wing shapes. In addition, the new method performs as well as the old method when used to estimate natal dispersal distances of North American birds. The folded-wing method will allow for estimates of the total wing to be readily obtained from thousands of specimens in ornithological collections, thus providing critical information for studies of flight and dispersal in birds.

La dispersión es un proceso fundamental en evolución y ecología. Debido al papel predominante del vuelo en el movimiento de las aves, su capacidad de dispersión puede estimarse a partir de su morfología de vuelo. La mayoría de los predictores de la eficiencia de vuelo requieren una estimación del área total del ala, pero los métodos existentes para estimar el área del ala requieren numerosos pasos y son propensos a errores compuestos. En este estudio validamos un nuevo método para estimar el área total del ala que requiere solo la medida de la envergadura y dos medidas de las alas plegadas que pueden tomarse de pieles del estudio: el largo y el ancho del ala. Demostramos que el nuevo método estima el área total del ala con alta precisión en una variedad de grupos de aves y formas de alas. Además, el nuevo método funciona tan bien como el anterior cuando se usa para estimar las distancias de dispersión natal de las aves de América del Norte. El nuevo método permitirá obtener fácilmente estimaciones del área alar total a partir de miles de especímenes en colecciones ornitológicas, beneficiando estudios de vuelo y dispersión en aves.

Community Preventive Health Education Intervention for Pediatric Iron-Deficiency Anemia in Rural Southeast Nigeria.

Objectives: Iron-deficiency anemia (IDA) is a global cause of morbidity in children under five, particularly in sub-Saharan Africa. In southeast Nigeria, poor dietary intake and caregiver knowledge about childhood anemia are observed; however, there is no consensus on how to best prevent it. This study seeks to test the effectiveness of caregiver education on improving anemia knowledge and dietary prevention strategies and promoting sustainable lifestyle changes to reduce the prevalence of childhood IDA. Study Design: A questionnaire was administered to the primary caregivers of 41 patients under age five with anemia in southeast Nigeria regarding socioeconomic status (SES), diet diversity, and risk factors for anemia. Caregivers were administered a preeducation questionnaire, poster education on anemia and iron-rich foods, and a posteducation questionnaire. All patients underwent a medical exam to confirm a diagnosis of anemia or anemia-related conditions. Results: Ninety-five percent of patients had moderate diet diversity, but there was no correlation between diet diversity and SES. Barriers to healthier diets were associated with SES. Preeducation scores were not associated with caregivers' education levels; however, posteducation scores were significantly higher in university-educated than technical-trained caregivers. Caregiver-reported self-efficacy increased after the education program. Conclusion: Caregivers' SES was associated with financial and knowledge barriers to a healthier diet but not diet diversity, suggesting that nutritional education could benefit all SES groups. Overall, the education program increased caregivers' anemia knowledge across educational levels. A community-based health education program could improve caregivers' anemia knowledge and self-efficacy in applying this information and potentially reduce this area's pediatric IDA.

Benchmark datasets for SARS-CoV-2 surveillance bioinformatics.

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. Methods: We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study. Results: The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications; two were derived from data mining public databases to answer common questions not covered by published datasets; one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2. Discussion: The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines.

Effect of genetic background on the evolution of Vancomycin-Intermediate Staphylococcus aureus (VISA).

Vancomycin-intermediate Staphylococcus aureus (VISA) typically arises through accumulation of chromosomal mutations that alter cell-wall thickness and global regulatory pathways. Genome-based prediction of VISA requires understanding whether strain background influences patterns of mutation that lead to resistance. We used an iterative method to experimentally evolve three important methicillin-resistant S. aureus (MRSA) strain backgrounds-(CC1, CC5 and CC8 (USA300)) to generate a library of 120 laboratory selected VISA isolates. At the endpoint, isolates had vancomycin MICs ranging from 4 to 10 µg/mL. We detected mutations in more than 150 genes, but only six genes (already known to be associated with VISA from prior studies) were mutated in all three background strains (walK, prs, rpoB, rpoC, vraS, yvqF). We found evidence of interactions between loci (e.g., vraS and yvqF mutants were significantly negatively correlated) and rpoB, rpoC, vraS and yvqF were more frequently mutated in one of the backgrounds. Increasing vancomycin resistance was correlated with lower maximal growth rates (a proxy for fitness) regardless of background. However, CC5 VISA isolates had higher MICs with fewer rounds of selection and had lower fitness costs than the CC8 VISA isolates. Using multivariable regression, we found that genes differed in their contribution to overall MIC depending on the background. Overall, these results demonstrated that VISA evolved through mutations in a similar set of loci in all backgrounds, but the effect of mutation in common genes differed with regard to fitness and contribution to resistance in different strains.

Genomic analysis of variability in Delta-toxin levels between Staphylococcus aureus strains.

BACKGROUND: The delta-toxin (δ-toxin) of Staphylococcus aureus is the only hemolysin shown to cause mast cell degranulation and is linked to atopic dermatitis, a chronic inflammatory skin disease. We sought to characterize variation in δ-toxin production across S. aureus strains and identify genetic loci potentially associated with differences between strains. METHODS: A set of 124 S. aureus strains was genome-sequenced and δ-toxin levels in stationary phase supernatants determined by high performance liquid chromatography (HPLC). SNPs and kmers were associated with differences in toxin production using four genome-wide association study (GWAS) methods. Transposon mutations in candidate genes were tested for their δ-toxin levels. We constructed XGBoost models to predict toxin production based on genetic loci discovered to be potentially associated with the phenotype. RESULTS: The S. aureus strain set encompassed 40 sequence types (STs) in 23 clonal complexes (CCs). δ-toxin production ranged from barely detectable levels to >90,000 units, with a median of >8,000 units. CC30 had significantly lower levels of toxin production than average while CC45 and CC121 were higher. MSSA (methicillin sensitive) strains had higher δ-toxin production than MRSA (methicillin resistant) strains. Through multiple GWAS approaches, 45 genes were found to be potentially associated with toxicity. Machine learning models using loci discovered through GWAS as features were able to predict δ-toxin production (as a high/low binary phenotype) with a precision of .875 and specificity of .990 but recall of .333. We discovered that mutants in the carA gene, encoding the small chain of carbamoyl phosphate synthase, completely abolished toxin production and toxicity in Caenorhabditis elegans. CONCLUSIONS: The amount of stationary phase production of the toxin is a strain-specific phenotype likely affected by a complex interaction of number of genes with different levels of effect. We discovered new candidate genes that potentially play a role in modulating production. We report for the first time that the product of the carA gene is necessary for δ-toxin production in USA300. This work lays a foundation for future work on understanding toxin regulation in S. aureus and prediction of phenotypes from genomic sequences.

TLR-exosomes exhibit distinct kinetics and effector function.

The innate immune system is vital to rapidly responding to pathogens and Toll-like receptors (TLRs) are a critical component of this response. Nanovesicular exosomes play a role in immunity, but to date their exact contribution to the dissemination of the TLR response is unknown. Here we show that exosomes from TLR stimulated cells can largely recapitulate TLR activation in distal cells in vitro. We can abrogate the action-at-a-distance signaling of exosomes by UV irradiation, demonstrating that RNA is crucial for their effector function. We are the first to show that exosomes derived from poly(I:C) stimulated cells induce in vivo macrophage M1-like polarization within murine lymph nodes. These poly(I:C) exosomes demonstrate enhanced trafficking to the node and preferentially recruit neutrophils as compared to control exosomes. This work definitively establishes the differential effector function for exosomes in communicating the TLR activation state of the cell of origin.

Neonatal overnutrition in mice exacerbates high-fat diet-induced metabolic perturbations.

Neonatal overnutrition results in accelerated development of high-fat diet (HFD)-induced metabolic defects in adulthood. To understand whether the increased susceptibility was associated with aggravated inflammation and dysregulated lipid metabolism, we studied metabolic changes and insulin signaling in a chronic postnatal overnutrition (CPO) mouse model. Male Swiss Webster pups were raised with either three pups per litter to induce CPO or ten pups per litter as control (CTR) and weaned to either low-fat diet (LFD) or HFD. All animals were killed on the postnatal day 150 (P150) except for a subset of mice killed on P15 for the measurement of stomach weight and milk composition. CPO mice exhibited accelerated body weight gain and increased body fat mass prior to weaning and the difference persisted into adulthood under conditions of both LFD and HFD. As adults, insulin signaling was more severely impaired in epididymal white adipose tissue (WAT) from HFD-fed CPO (CPO-HFD) mice. In addition, HFD-induced upregulation of pro-inflammatory cytokines was exaggerated in CPO-HFD mice. Consistent with greater inflammation, CPO-HFD mice showed more severe macrophage infiltration than HFD-fed CTR (CTR-HFD) mice. Furthermore, when compared with CTR-HFD mice, CPO-HFD mice exhibited reduced levels of several lipogenic enzymes in WAT and excess intramyocellular lipid accumulation. These data indicate that neonatal overnutrition accelerates the development of insulin resistance and exacerbates HFD-induced metabolic defects, possibly by worsening HFD-induced inflammatory response and impaired lipid metabolism.