Retrospective evaluation of an integrated molecular-epidemiological approach to cyclosporiasis outbreak investigations - United States, 2021.

Cyclosporiasis results from an infection of the small intestine by Cyclospora parasites after ingestion of contaminated food or water, often leading to gastrointestinal distress. Recent developments in temporally linking genetically related Cyclospora isolates demonstrated effectiveness in supporting epidemiological investigations. We used 'temporal-genetic clusters' (TGCs) to investigate reported cyclosporiasis cases in the United States during the 2021 peak-period (1 May - 31 August 2021). Our approach split 655 genotyped isolates into 55 genetic clusters and 31 TGCs. We linked two large multi-state epidemiological clusters (Epidemiologic Cluster 1 [n = 136 cases, 54 genotyped] and Epidemiologic Cluster 2 [n = 42 cases, 15 genotyped]) to consumption of lettuce varieties; however, product traceback did not identify a specific product for either cluster due to the lack of detailed product information. To evaluate the utility of TGCs, we performed a retrospective case study comparing investigation outcomes of outbreaks first detected using epidemiological methods with those of the same outbreaks had TGCs been used to first detect them. Our study results indicate that adjustments to routine epidemiological approaches could link additional cases to epidemiological clusters of cyclosporiasis. Overall, we show that CDC's integrated genotyping and epidemiological investigations provide valuable insights into cyclosporiasis outbreaks in the United States.

Evaluation of various distance computation methods for construction of haplotype-based phylogenies from large MLST datasets.

Multi-locus sequence typing (MLST) is widely used to investigate genetic relationships among eukaryotic taxa, including parasitic pathogens. MLST analysis workflows typically involve construction of alignment-based phylogenetic trees - i.e., where tree structures are computed from nucleotide differences observed in a multiple sequence alignment (MSA). Notably, alignment-based phylogenetic methods require that all isolates/taxa are represented by a single sequence. When multiple loci are sequenced these sequences may be concatenated to produce one tree that includes information from all loci. Alignment-based phylogenetic techniques are robust and widely used yet possess some shortcomings, including how heterozygous sites are handled, intolerance for missing data (i.e., partial genotypes), and differences in the way insertions-deletions (indels) are scored/treated during tree construction. In certain contexts, 'haplotype-based' methods may represent a viable alternative to alignment-based techniques, as they do not possess the aforementioned limitations. This is namely because haplotype-based methods assess genetic similarity based on numbers of shared (i.e., intersecting) haplotypes as opposed to similarities in nucleotide composition observed in an MSA. For haplotype-based comparisons, choosing an appropriate distance statistic is fundamental, and several statistics are available to choose from. However, a comprehensive assessment of various available statistics for their ability to produce a robust haplotype-based phylogenetic reconstruction has not yet been performed. We evaluated seven distance statistics by applying them to extant MLST datasets from the gastrointestinal parasite Cyclospora cayetanensis and two species of pathogenic nematode of the genus Strongyloides. We compare the genetic relationships identified using each statistic to epidemiologic, geographic, and host metadata. We show that Barratt's heuristic definition of genetic distance was the most robust among the statistics evaluated. Consequently, it is proposed that Barratt's heuristic represents a useful approach for use in the context of challenging MLST datasets possessing features (i.e., high heterozygosity, partial genotypes, and indel or repeat-based polymorphisms) that confound or preclude the use of alignment-based methods.

Parental Mediation Moderates the Association Between Social Media Exposure and Tobacco and Alcohol Use: Differences Between Elementary and Middle School Students.

OBJECTIVE: With the popularity of social media among adolescents, the relation between social media exposure (especially exposure to undesirable content) and adolescent tobacco and alcohol use has attracted much attention. This study examined the association between social media exposure and tobacco and alcohol use, as well as the moderating role of parental active mediation and restrictive mediation; differences between elementary and middle school students were also investigated. METHOD: A total of 697 elementary school students ages 9-13 and 794 middle school students ages 12-18 were recruited to complete a questionnaire survey. RESULTS: Social media exposure was positively associated with tobacco and alcohol use among both elementary and middle school students. For elementary school students, both active mediation and restrictive mediation moderated the association between social media exposure and tobacco and alcohol use; for middle school students, neither of these moderating effects was significant. CONCLUSIONS: Findings suggest that social media exposure is a risk factor for both elementary and middle school students. Both parental active and restrictive mediation are promising targets for intervention because they can mitigate the risk of social media exposure for elementary school students. However, further research should focus on factors that effectively buffer the negative effects of social media exposure on tobacco and alcohol use among middle school students.

Development and Validation of an Autonomy Questionnaire for Chinese Adolescents From the Perspective of Network Culture.

This study developed a measure of autonomy for adolescents in contemporary China. First, data from 44 interviewees-40 secondary school students, 2 parents, and 2 secondary school teachers-were used to explore the connotation and theoretical structure of autonomy in adolescents in China. Next, a preliminary Adolescent Autonomy Questionnaire was created from the interview data and administered to 775 secondary school students. Exploratory factor analysis and confirmatory factor analysis (CFA) were conducted to verify the factor structure. Finally, 614 secondary school students completed the Adolescent Autonomy Questionnaire, Personal Growth Initiative Scale-II, and Adolescence Ego Identity Crisis Scale to evaluate criterion validity. The final version of the Adolescent Autonomy Questionnaire included 16 items and four subscales: autonomous decision-making, autonomous regulation, autonomous protection, and autonomous problem-solving. The total variance of the cumulative interpretation questionnaire was 62.54%. The CFA results showed that the four-factor model fits the data well: χ 2/df = 2.340, CFI = 0.949, RMSEA = 0.042, SRMR = 0.046. Evaluation of the psychometric properties of the Adolescent Autonomy Questionnaire provided support for the reliability and validity of the measure. Thus, it serves as an effective measurement tool for assessing the autonomy of adolescents in China.

Cutaneous Leishmaniasis Caused by an Unknown Leishmania Strain, Arizona, USA.

We investigated an autochthonous case of cutaneous leishmaniasis caused by a genetically different Leishmania sp. in a patient in Arizona, USA. This parasite was classified into the subgenus Leishmania on the basis of multilocus DNA sequence and phylogenetic analyses of the rRNA locus and 11 reference genes.

Chromosome-Level Genome Sequence of Leishmania (Leishmania) tropica Strain CDC216-162, Isolated from an Afghanistan Clinical Case.

PacBio and Illumina MiSeq platforms were used for genomic sequencing of a Leishmania (Leishmania) tropica strain isolated from a patient infected in Pakistan. PacBio assemblies were generated using Flye v2.4 and polished with MiSeq data. The results represent a considerable improvement of the currently available genome sequences in the GenBank database.

Upward social comparison and state anxiety as mediators between passive social network site usage and online compulsive buying among women.

Although Social Network Site (SNS) usage has been shown to be related to online compulsive buying among women, little is known about the mediating mechanisms underlying this association. Based on the Interaction of Person-Affect-Cognition-Execution model (I-PACE) for addictive behaviors and social comparison theory, the present study examined the mediating roles of upward social comparison and state anxiety in the link between passive SNS usage and online compulsive buying among female undergraduate students. A sample of 799 Chinese female undergraduate students (mean age = 19.86 years, SD = 1.63) were recruited to complete questionnaires measuring passive SNS usage, upward social comparison on SNS, state anxiety, and online compulsive buying. After controlling for online shopping experience, the results showed that passive SNS usage was positively associated with online compulsive buying; upward social comparison and state anxiety partially mediated this link, which contained three mediating pathways - the separate mediating effect of upward social comparison and state anxiety, and the sequential mediating effect of upward social comparison and state anxiety. These findings can advance our understanding of how passive SNS usage is related to online compulsive buying among female undergraduate students. Limitations and implications of this study are discussed.

Draft Genome Sequences of Leishmania (Leishmania) amazonensis, Leishmania (Leishmania) mexicana, and Leishmania (Leishmania) aethiopica, Potential Etiological Agents of Diffuse Cutaneous Leishmaniasis.

We present here the draft genome sequences of Leishmania (Leishmania) amazonensis, Leishmania (Leishmania) mexicana, and Leishmania (Leishmania) aethiopica, potential etiological agents of diffuse cutaneous leishmaniasis (DCL). Sequence data were obtained using PacBio and MiSeq platforms. The PacBio assemblies generated using Canu v1.6 are more contiguous than are those in the available data.

First Draft Genome Sequence of Leishmania (Viannia) lainsoni Strain 216-34, Isolated from a Peruvian Clinical Case.

We present here the first draft genome sequence of Leishmania (Viannia) lainsoni strain 216-34, sequenced using PacBio and MiSeq platforms. PacBio contigs were generated from de novo assemblies using CANU version 1.6 and polished using Illumina reads.

Draft Genome Sequence of French Guiana Leishmania (Viannia) guyanensis Strain 204-365, Assembled Using Long Reads.

We present here the draft genome sequence for Leishmania (Viannia) guyanensis. The isolate was obtained from a clinical case of cutaneous leishmaniasis in French Guiana. Genomic DNA was sequenced using PacBio and MiSeq platforms.

Efficient detection of viral transmissions with Next-Generation Sequencing data.

BACKGROUND: Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Molecular analysis has been frequently used in the study of HCV outbreaks and transmission chains; helping identify a cluster of sequences as linked by transmission if their genetic distances are below a previously defined threshold. However, HCV exists as a population of numerous variants in each infected individual and it has been observed that minority variants in the source are often the ones responsible for transmission, a situation that precludes the use of a single sequence per individual because many such transmissions would be missed. The use of Next-Generation Sequencing immensely increases the sensitivity of transmission detection but brings a considerable computational challenge because all sequences need to be compared among all pairs of samples. METHODS: We developed a three-step strategy that filters pairs of samples according to different criteria: (i) a k-mer bloom filter, (ii) a Levenhstein filter and (iii) a filter of identical sequences. We applied these three filters on a set of samples that cover the spectrum of genetic relationships among HCV cases, from being part of the same transmission cluster, to belonging to different subtypes. RESULTS: Our three-step filtering strategy rapidly removes 85.1% of all the pairwise sample comparisons and 91.0% of all pairwise sequence comparisons, accurately establishing which pairs of HCV samples are below the relatedness threshold. CONCLUSIONS: We present a fast and efficient three-step filtering strategy that removes most sequence comparisons and accurately establishes transmission links of any threshold-based method. This highly efficient workflow will allow a faster response and molecular detection capacity, improving the rate of detection of viral transmissions with molecular data.

Enhancing human spermine synthase activity by engineered mutations.

Spermine synthase (SMS) is an enzyme which function is to convert spermidine into spermine. It was shown that gene defects resulting in amino acid changes of the wild type SMS cause Snyder-Robinson syndrome, which is a mild-to-moderate mental disability associated with osteoporosis, facial asymmetry, thin habitus, hypotonia, and a nonspecific movement disorder. These disease-causing missense mutations were demonstrated, both in silico and in vitro, to affect the wild type function of SMS by either destabilizing the SMS dimer/monomer or directly affecting the hydrogen bond network of the active site of SMS. In contrast to these studies, here we report an artificial engineering of a more efficient SMS variant by transferring sequence information from another organism. It is confirmed experimentally that the variant, bearing four amino acid substitutions, is catalytically more active than the wild type. The increased functionality is attributed to enhanced monomer stability, lowering the pKa of proton donor catalytic residue, optimized spatial distribution of the electrostatic potential around the SMS with respect to substrates, and increase of the frequency of mechanical vibration of the clefts presumed to be the gates toward the active sites. The study demonstrates that wild type SMS is not particularly evolutionarily optimized with respect to the reaction spermidine → spermine. Having in mind that currently there are no variations (non-synonymous single nucleotide polymorphism, nsSNP) detected in healthy individuals, it can be speculated that the human SMS function is precisely tuned toward its wild type and any deviation is unwanted and disease-causing.

Energy Transfer in a Nanoscale Multichromophoric System: Fluorescent Dye-Doped Conjugated Polymer Nanoparticles.

We report on the fluorescence properties and the combined effects of energy diffusion and energy transfer in polyfluorene nanoparticles doped with a variety of fluorescent dyes. As the doping host, polyfluorene possesses extraordinary "light harvesting" ability, resulting in higher per-particle brightness as compared to dye-loaded silica nanoparticles of similar dimensions. Both the steady-state fluorescence spectra and time-resolved fluorescence measurements indicate highly efficient energy transfer from the host polymer to the acceptor dye molecules. A model that takes into account the combined effects of energy diffusion, Förster transfer, and particle size was developed. Comparisons of experimental data to the model results elucidate the importance of particle size and energy diffusion within the polymer in determining the optical properties of the doped conjugated polymer nanoparticles. Fluorescence quantum yields of ~40% and peak extinction coefficients of 1.5 × 10(9) M(-1)cm(-1) were determined for aqueous suspensions of ~30 nm diameter polymer nanoparticles doped with perylene or coumarin 6 (2 wt %). Photobleaching experiments indicate that energy transfer phenomena strongly influence the photostability of these dye-doped nanoparticles. Significant features of these nanoparticles include the high brightness, highly red-shifted emission spectrum, and excellent photostability, which are promising for biological labeling and sensing applications. In addition, the nanoparticles are a useful model system for studying energy transfer in dense, nanostructured, multichromophoric systems.