Red filter meibography by smartphones in patients with meibomian gland dysfunction: a validity and reliability study.

OBJECTIVE: The objective of this study is to determine the validity and reliability of the red filter meibography by smartphone compared with infrared in assessing meibomian gland drop-out. METHODS AND ANALYSIS: An analytical cross-sectional study was done with a total of 35 subjects (68 eyes) with suspected MGD based on symptoms and lid morphological abnormalities. Meibomian glands were photographed using two smartphones (Samsung S9 and iPhone XR) on a slit-lamp with added red filter. Images were assessed subjectively using meiboscore by the two raters and drop-out percentages were assessed by ImageJ. RESULTS: There was no agreement in meiboscore and a minimal level of agreement in drop-out percentages between red filter meibography and infrared. Inter-rater reliability showed no agreement between two raters. Intra-rater reliability demonstrated weak agreement in rater 1 and no agreement in rater 2. CONCLUSION: Validity of the red filter meibography technique by smartphones is not yet satisfactory in evaluating drop-out. Further improvement on qualities of images must be done and research on subjective assessment was deemed necessary due to poor results of intrarater and inter-rater reliability.

Assessment of the integrated disease surveillance and response system implementation in health zones at risk for viral hemorrhagic fever outbreaks in North Kivu, Democratic Republic of the Congo, following a major Ebola outbreak, 2021.

BACKGROUND: The Democratic Republic of the Congo (DRC) experienced its largest Ebola Virus Disease Outbreak in 2018-2020. As a result of the outbreak, significant funding and international support were provided to Eastern DRC to improve disease surveillance. The Integrated Disease Surveillance and Response (IDSR) strategy has been used in the DRC as a framework to strengthen public health surveillance, and full implementation could be critical as the DRC continues to face threats of various epidemic-prone diseases. In 2021, the DRC initiated an IDSR assessment in North Kivu province to assess the capabilities of the public health system to detect and respond to new public health threats. METHODS: The study utilized a mixed-methods design consisting of quantitative and qualitative methods. Quantitative assessment of the performance in IDSR core functions was conducted at multiple levels of the tiered health system through a standardized questionnaire and analysis of health data. Qualitative data were also collected through observations, focus groups and open-ended questions. Data were collected at the North Kivu provincial public health office, five health zones, 66 healthcare facilities, and from community health workers in 15 health areas. RESULTS: Thirty-six percent of health facilities had no case definition documents and 53% had no blank case reporting forms, limiting identification and reporting. Data completeness and timeliness among health facilities were 53% and 75% overall but varied widely by health zone. While these indicators seemingly improved at the health zone level at 100% and 97% respectively, the health facility data feeding into the reporting structure were inconsistent. The use of electronic Integrated Disease Surveillance and Response is not widely implemented. Rapid response teams were generally available, but functionality was low with lack of guidance documents and long response times. CONCLUSION: Support is needed at the lower levels of the public health system and to address specific zones with low performance. Limitations in materials, resources for communication and transportation, and workforce training continue to be challenges. This assessment highlights the need to move from outbreak-focused support and funding to building systems that can improve the long-term functionality of the routine disease surveillance system.

Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration.

In this study, we synthesized novel α,ß-unsaturated 2-cyanoacetamide derivatives (1-5) using microwave-assisted Knoevenagel condensation. Characterization of these compounds was carried out using FTIR and 1H NMR spectroscopy. We then evaluated their in vitro antibacterial activity against both gram-positive and gram-negative pathogenic bacteria. Additionally, we employed in silico methods, including ADMET prediction and density functional theory (DFT) calculations of molecular orbital properties, to investigate these cyanoacetamide derivatives (1-5). Molecular docking was used to assess the binding interactions of these derivatives (1-5) with seven target proteins (5MM8, 4NZZ, 7FEQ, 5NIJ, ITM2, 6SE1, and 5GVZ) and compared them to the reference standard tyrphostin AG99. Notably, derivative 5 exhibited the most favorable binding affinity, with a binding energy of -7.7 kcal mol-1 when interacting with the staphylococcus aureus (PDB:5MM8), while also meeting all drug-likeness criteria. Additionally, molecular dynamics simulations were carried out to evaluate the stability of the interaction between the protein and ligand, utilizing parameters such as Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), Radius of Gyration (Rg), and Principal Component Analysis (PCA). A 50 nanosecond molecular dynamics (MD) simulation was performed to investigate stability further, incorporating RMSD and RMSF analyses on compound 5 within the active binding site of the modeled protein across different temperatures (300, 305, 310, and 320 K). Among these temperatures, compound 5 exhibited an RMSD value ranging from approximately 0.2 to 0.3 nm at 310 K (body temperature) with the 5MM8 target, which differed from the other temperature conditions. The in silico results suggest that compound 5 maintained significant conformational stability throughout the 50 ns simulation period. It is consistent with its low docking energy and in vitro findings concerning α,ß-unsaturated cyanoacetamides. Key insights from this study include:•The creation of innovative α,ß-unsaturated 2-cyanoacetamide derivatives (1-5) employing cost-effective, licensed, versatile, and efficient software for both in silico and in vitro assessment of antibacterial activity.•Utilization of FTIR and NMR techniques for characterizing compounds 1-5.

Investigating gastrointestinal disorders in pregnancy.

This article reviews anatomical and physiological changes and alterations in reference intervals for laboratory tests in healthy pregnancy, pertinent to investigation of the gastrointestinal system. The safety of procedures and radiological investigations relevant to the investigation of gastrointestinal disorders in pregnancy are also reviewed.

Two cases of diquat poisoning in adolescent children.

Diquat (DQ) is among the most widely used herbicides, and its intake can cause severe systemic toxicity that manifests rapidly. The resultant symptoms can cause the dysfunction of a range of tissues and organs,. As there is no specific antidote for diquat poisoning and the efficacy of extant treatments is suboptimal, physicians must acquire a more comprehensive understanding of the most effective approaches to managing affected patients. Relative few studies have been published to date focused on diquat poisoning in pediatric patients. In this report, we compare two similar cases of juvenile diquat poisoning with dynamic changes in clinical manifestations, laboratory values, and imaging results. For the first time, the difference in whether to perform blood flow perfusion and the time difference of initiation of hemoperfusion had a clear clinical difference in the subsequent effects of diquat poisoning in children with diquat poisoning. Limited evidence is available regarding the efficacy of early hemoperfusion for diquat poisoning; however, the differences in clinical outcomes articulated here highlight the benefits of early and timely hemoperfusion therapy in the treatment of DQ toxicity in children, in conjunction with primary supportive care in the management of DQ poisoning in children.

Global Measles Surveillance: Trends, Challenges, and Implications for Public Health Interventions.

Measles, a highly contagious disease primarily affecting children, carries serious health risks, including complications and mortality. Vaccination remains the most effective preventive measure against measles transmission. The COVID-19 pandemic has exacerbated challenges in surveillance and immunization efforts, leaving millions of people exposed to preventable diseases such as measles. Globally accelerated immunization campaigns are critical for achieving regional elimination goals and mitigating the risk of outbreaks. Our team has developed an open-access database for global measles monitoring, facilitating standardized data collection and analysis. The analysis of measles cases from 2011 to 2023 reveals fluctuating trends, with notable increases in Africa in 2019 and 2023, indicating potential gaps in control strategies. Using an automated signal detection tool developed by the European Centre for Disease Prevention and Control (ECDC) team, we identified significant variations between World Health Organization (WHO) regions, underscoring the importance of continuous monitoring to detect epidemiological changes early. These results underscore the need for robust surveillance systems and accelerated vaccination efforts to safeguard public health.

Sexual dimorphism and topological variability in fingerprint ridge density in a north-west Indian population.

The science of fingerprints is very crucial in criminal investigation as it helps identify perpetrators or victims of a crime. Fingerprint ridge density (FPRD), which refers to the number of ridges within a specific area on the epidermal skin layer of the distal phalanges in humans, has been found to differ between males and females. This study attempts to estimate the sex from FPRD and evaluates the diversity in FPRD across several topological areas. The study involves 208 participants (120 males, 88 females) between the ages 18 to 25 years from a North-west Indian population. Fingerprints were collected, and FPRD was accessed in radial, ulnar, and proximal areas as recommended by Gutierrez-Redomero et al. (Forensic Sci Int 180(1):17-22, 2008). FPRD has been quantified using the techniques described by Acree (Forensic Sci Int 102(1):35-44, 1999). When evaluating FPRD in the lateral pocket loops and twin loops, the proximal-side core was considered. The study reveals that males have a mean fingerprint ridge density of 12.82 ridges/25 mm2 while females have 13.01 ridges/25 mm2. Females have higher fingerprint ridge density solely in the proximal area; males have higher fingerprint ridge density in both radial and ulnar areas. In conclusion, this research underscores the potential of fingerprint ridge density as a parameter for investigating population variations and individual identification. Future studies on fingerprint ridge density in India's diverse population will help establish reference ranges, allowing for sex and likely population group estimation, making it a valuable tool for preliminary examinations and exclusion criteria for sex estimation in crime scene investigations.

PFAS Contamination in Europe: Generating Knowledge and Mapping Known and Likely Contamination with "Expert-Reviewed" Journalism.

While the extent of environmental contamination by per- and polyfluoroalkyl substances (PFAS) has mobilized considerable efforts around the globe in recent years, publicly available data on PFAS in Europe were very limited. In an unprecedented experiment of "expert-reviewed journalism" involving 29 journalists and seven scientific advisers, a cross-border collaborative project, the "Forever Pollution Project" (FPP), drew on both scientific methods and investigative journalism techniques such as open-source intelligence (OSINT) and freedom of information (FOI) requests to map contamination across Europe, making public data that previously had existed as "unseen science". The FPP identified 22,934 known contamination sites, including 20 PFAS manufacturing facilities, and 21,426 "presumptive contamination sites", including 13,745 sites presumably contaminated with fluorinated aqueous film-forming foam (AFFF) discharge, 2911 industrial facilities, and 4752 sites related to PFAS-containing waste. Additionally, the FPP identified 231 "known PFAS users", a new category for sites with an intermediate level of evidence of PFAS use and considered likely to be contamination sources. However, the true extent of contamination in Europe remains significantly underestimated due to a lack of comprehensive geolocation, sampling, and publicly available data. This model of knowledge production and dissemination offers lessons for researchers, policymakers, and journalists about cross-field collaborations and data transparency.

[Resources and utilization of medicinal plants in countries and regions involved in "the Belt and Road" Initiative].

The protection, development, and utilization of medicinal plant resources are important cornerstones of maintaining human health. However, due to factors such as the reduction of high-quality land resources, deterioration of ecological environments, and excessive and disorderly resource development, medicinal plant resources are becoming scarce, and some of them are insufficiently supplied. With the proposal of "the Belt and Road" Initiative, the cooperation between China and "the Belt and Road" partners(the countries and regions involved in "the Belt and Road" Initiative)is increasingly close, which provides a new opportunity for carrying out trade of medicinal plant resources and alleviating the problem of imbalance and relative inadequacy of medicinal plant resources in countries. This study first determined the distribution and species information of plant resources in countries and regions involved in "the Belt and Road" Initiative by investigating the database of plant distribution and that of medicinal plant resources. Then, according to the published data from the International Union for Conservation of Nature(IUCN) and the Convention on International Trade in Endangered Species of Wild Fauna and Flora(CITES), this study identified the rare and endangered medicinal plants and the medicinal plants under trade control in countries and regions involved in "the Belt and Road" Initiative and finally sorted out the list of potential medicinal plant resources in countries and regions involved in "the Belt and Road" Initiative that can be used by China. This data resource can not only be used for the overall protection of important endangered species but also scientifically guide the development and utilization of medicinal resources, providing guidance and a theoretical basis for the sustainable development of medicinal plant resources in countries and regions involved in "the Belt and Road" Initiative.

Biochemical Abnormalities Associated With Sudden Infant Death Syndrome: A Case Report.

Sudden infant death is a complex event characterized by biochemical features that are difficult to understand in general settings. Herein, we present a case report of a three-month-old infant who succumbed to sudden infant death syndrome (SIDS), focusing on the biochemical abnormalities identified through post-mortem analysis. The infant, previously healthy and meeting developmental milestones, was found lifeless in the crib during sleep. An autopsy revealed no anatomical abnormalities or signs of external trauma, consistent with SIDS diagnosis. Biochemical analysis of SIDS continued after post-mortem samples revealed dysregulation in neurotransmitter pathways, particularly serotonin, within the brain stem. These findings suggest a potential disruption in serotonin signaling, which may contribute to the vulnerability of infants to sudden death during sleep. Furthermore, metabolic profiling revealed deficiencies in enzymes involved in mitochondrial energy metabolism, particularly those related to fatty acid oxidation. These metabolic disturbances may compromise cellular function and contribute to the pathogenesis of SIDS. Environmental factors were also explored, with analysis revealing elevated levels of nicotine metabolites in post-mortem samples, suggesting maternal smoking exposure during pregnancy. Nicotine and its derivatives have known effects on neurotransmitter systems, potentially exacerbating underlying biochemical vulnerabilities in susceptible infants. This case report underscores the complex interplay of biochemical factors in the pathogenesis of SIDS and highlights the importance of multidisciplinary approaches in unraveling its mysteries. Further research is warranted to elucidate the precise mechanisms underlying these biochemical abnormalities and to develop targeted interventions aimed at reducing the incidence of SIDS and safeguarding infant health.

Improving state medicolegal death investigation: Does system level reform improve public health data concerning drug-related mortality?

In the United States, the governance of unnatural death certification varies greatly by state. Although cross-sectional research has linked mortality data quality with variation in medicolegal death investigation systems across states-especially with regards to drug-related deaths-this relationship has not be sufficiently tested using longitudinal data. This research assesses the impact of system governance reform on the quality of drug mortality data by assessing the impact of transitioning from a coroner system to a medical examiner system on data quality. The research finds no evidence that system-level reform is associated with improved drug-related mortality data quality. These findings suggest that alternative methods should be examined for improving public health data concerning drug-related mortality. These likely include focusing on individual-level characteristics and practices of officials and offices, rather than system-level variables.

Quadrat soil pollen signal reflects plant important values in forests and shrublands from subtropical China.

Pollen analysis, a crucial tool in botany and ecology for examining historical biotic dynamics, has elicited debate owing to its complex link with vegetation. The challenge lies in discerning the ecological significance of pollen data. In this study, we conducted detailed quadrat surveys on Jinhua Mountain, subtropical China, analyzing topsoil pollen to determine whether pollen signals accurately reflect key ecological components in the forests and shrublands. We performed direct comparisons between pollen and plant compositions and calculated pollen percentages and plant Important Values (IVs) for each quadrat. The results indicate greater homogeneity in pollen composition across the study area compared to plant composition, particularly in the high percentage of Pinus pollen. However, distinct plant communities exhibited significantly different pollen compositions, as evidenced by the multi-response permutation test. This divergence aligns with variations in the dominant plant species across different communities. There were significant correlations between pollen percentages and plant IVs, with correlation coefficients of 0.55 (p < 0.001) at the quadrat level and 0.78 (p < 0.001) at the taxon level. These results support the utility of pollen analysis for representing ecologically significant values in subtropical Chinese forests and shrublands. Such correlations might also be extrapolated to pollen-based paleoecological studies.

Trauma behind the keyboard: Exploring disparities in child sexual abuse materials exposure and mental health factors among investigators and forensic examiners - A network analysis.

BACKGROUND: Despite acknowledging the detrimental impact of child sexual abuse material (CSAM) exposure on the mental and physical well-being of investigators and forensic examiners, there is a need for comprehensive exploration into the complex relationship between CSAM exposure, its various dimensions, mental health (i.e., anxiety, depression, and PTSD), and burnout, as well as the presence of positive attitudes towards the job. OBJECTIVE: To understand how CSAM exposure, mental health and burnout interconnect and cluster within distinct networks of police investigators and forensic examiners. PARTICIPANTS AND SETTING: Police investigators and forensic examiners from across the United States who were exposed to CSAM as part of their professions (N = 470). METHODS: Participants, recruited through connections with the National Criminal Justice Training Center, completed an anonymous online survey. RESULTS: The network analysis revealed differences in centrality between investigators and forensic examiners, particularly in their associations with exposure factors and mental health variables. Edges invariance tests showed differences in the strength of these associations, with some factors being more strongly linked to PTSD avoidance symptoms among investigators and others among forensic examiners. Stability analyses suggested potentially greater heterogeneity among investigators, while both groups displayed high stability in other centrality indices. CONCLUSIONS: This study contributes to our comprehension of the distinct experiences and challenges faced by CSAM investigators and forensic examiners, and specifically the nuanced disparities between CSAM investigators and forensic examiners in terms of their exposure to CSAM content and the associated mental health factors. These insights highlight the imperative need for tailored support mechanisms and interventions that can effectively address the unique challenges encountered by individuals working tirelessly in this critical field.

Anti-inflammatory steroids from the South China Sea Sponge Spongia officinalis.

One new highly degraded steroid, namely 21-nor-4-ene-chaxine A (1) furnishing a 5/6/5-tricyclic, along with one known related analogue (2), were isolated from the South China Sea sponge Spongia officinalis. Their structures including absolute configurations were established by extensive spectroscopic data analysis, TDDFT-ECD calculation, and comparison with the spectral data previously reported in the literature. Compound 1 represent the new member of incisterols family with a highly degradation in ring B. In vitro bioassays revealed compound 2 exhibited significant anti-microglial inflammatory effect on lipopolysaccharide (LPS)-induced inflammation in BV-2 microglial cells.

Formaldehyde Exposure of Aquaculture Workers in Korea.

OBJECTIVES: Korea's aquaculture sector primarily cultivates aquatic life, with fish seed production as a focus. Formalin, a parasiticide, consists of 37% formaldehyde mixed with yellow No. 4 dye. Formaldehyde vaporization poses cancer risks, classified as a carcinogen. Korea regulates formaldehyde as a hazardous substance, requiring workplace environment measurements. Few aquaculture farms have conducted these checks in recent years. In this study, we investigated actual formaldehyde exposure levels among Korean aquaculture workers, highlighting a critical safety concern. METHODS: A field survey was conducted to measure formaldehyde exposure at 10 aquaculture farms in areas where Korean aquaculture is concentrated. Short-term and long-term personal samples, local samples, and direct-reading measurements were conducted. Formaldehyde exposure levels were detected in short-term personal samples from six farms and in long-term personal samples from two farms, and formaldehyde was detected in all local samples. In direct-reading measurements, a high concentration of formaldehyde was sustained for short periods. RESULTS: Long-term (8-hour) personal samples were mostly non-detectable, except for farms A and D, which had levels of 0.0009 ppm and 0.0017 ppm, respectively. Short-term (15-minute) samples were non-detectable in four farms, with an average of 0.0158 (±0.0130) ppm in the remaining six farms. Local samples from all farms had an average of 0.0384 (±0.0957) ppm of formaldehyde. For farms A and D, where long-term sampling detected formaldehyde, real-time measurements showed a sustained high concentration in farm A for about 48 minutes before decreasing. Farm D had no detectable formaldehyde throughout the monitoring period. CONCLUSION: According to the formaldehyde exposure level assessment, short term exposure to formaldehyde during and immediately after application of formalin nearly exceeded the ACGIH TLV STEL in one farm. However, concentration of long term samples appeared at 10% of ACGIH TLV TWA. Additional study is recommended to determine whether exposure to formaldehyde poses a health risk for aquaculture workers during application of formalin.

Mathematical modelling of clonal reduction therapeutic strategies in acute myeloid leukemia.

Over the years, the overall survival of older patients diagnosed with acute myeloid leukemia (AML) has not significantly increased. Although standard cytotoxic therapies that rapidly eliminate dividing myeloblasts are used to induce remission, relapse can occur due to surviving therapy-resistant leukemic stem cells (LSCs). Hence, anti-LSC strategies have become a key target to cure AML. We have recently shown that previously approved cardiac glycosides and glucocorticoids target LSC-enriched CD34+ cells in the primary human AML 8227 model with more efficacy than normal hematopoietic stem cells (HSCs). To translate these in vitro findings into humans, we developed a mathematical model of stem cell dynamics that describes the stochastic evolution of LSCs in AML post-standard-of-care. To this, we integrated population pharmacokinetic-pharmacodynamic (PKPD) models to investigate the clonal reduction potential of several promising candidate drugs in comparison to cytarabine, which is commonly used in high doses for consolidation therapy in AML patients. Our results suggest that cardiac glycosides (proscillaridin A, digoxin and ouabain) and glucocorticoids (budesonide and mometasone) reduce the expansion of LSCs through a decrease in their viability. While our model predicts that effective doses of cardiac glycosides are potentially too toxic to use in patients, simulations show the possibility of mometasone to prevent relapse through the glucocorticoid's ability to drastically reduce LSC population size. This work therefore highlights the prospect of these treatments for anti-LSC strategies and underlines the use of quantitative approaches to preclinical drug translation in AML.

Plant-mediated Z-scheme ZnO/TiO2-NCs for antibacterial potential and dye degradation: experimental and DFT study.

Efficient separation of electron-hole pairs remains pivotal in optimizing photogenerated carrier functionality across diverse catalytic and optoelectronic systems. This study presents the fabrication of a novel hollow direct Z-scheme photocatalyst, ZnO/TiO2. A thorough analysis encompassing various techniques such as Ultraviolet-Visible Spectroscopy (UV-Vis), X-ray Diffraction (XRD), Transmission electron Microscopy (TEM), Fourier Transform Infrared Spectroscopy (FT-IR), Thermogravimetric Analysis (TGA), and Energy-Dispersive X-ray Spectroscopy (EDX) provided detailed insights into the complex material characteristics of the ZnO/TiO2 heterojunction catalyst. The findings revealed coexisting anatase TiO2 and wurtzite ZnO phases, each retaining distinct attributes within the nanocomposites (NCs) structure. The study showcased the photocatalytic efficacy of ZnO/TiO2-NCs in decomposing Methylene Blue and Acridine Orange under UV irradiation, correlated with their underlying structures. Enhanced degradation of these dyes resulted from the establishment of a direct Z-scheme heterojunction between ZnO and TiO2. Employing Density Functional Theory (DFT) using Quantum ESPRESSO, this research analyzed phase diagrams and band structures, elucidating electronic properties and structural correlations. The study characterized a ZnO/TiO2 composite, revealing a band gap of 3.1-3.3 eV through UV-Visible spectroscopy and confirming its formation without impurity phases via XRD analysis. TEM and EDX showed uniform element dispersion (Zn: 27%, Ti: 29.62%, C: 5.03%, O: 38.35%). Computational analysis using DFT indicated a reduction in stable phases with increasing temperature. Enhanced dye degradation was observed (MB: 88.9%, AO: 84%), alongside significant antibacterial activity. In the future we predict that research will focus on development of scaled up production and photocatalytic activity through surface modification, while unveiling mechanistic insights and environmental applicability for multifunctional use in water treatment and antibacterial applications, leading to further advancement of the field.

Evaluation of in-house drug evidence testing by King County Medical Examiner's Office in "real-time" fatal overdose surveillance.

With the escalating overdose epidemic, many surveillance efforts have appeared. In 2018, King County Medical Examiner's Office (KCMEO) initiated a fatal overdose surveillance project aimed at expediting death certification and disseminating timely information. In this project, KCMEO investigators collected items of evidence of drug use from overdose death scenes, which were tested by five in-house methods, four using handheld devices: TruNarc Raman spectrometer, with and without the manufacture's H-Kit, Rigaku ResQ Raman spectrometer, and MX908 mass spectrometer. The fifth in-house method used fentanyl-specific urine test strips. Results from in-house testing were compared with results from Washington State Patrol (WSP) Materials Analysis Laboratory. From 2019 to 2022, there were 4244 evidence items of drugs and paraphernalia collected from 1777 deaths scenes. A total of 7526 in-house tests were performed on collected specimens, and 2153 tests were performed by the WSP laboratory using standard analytical methods. The WSP results served as reference standards to calculate performance metrics of the in-house methods. Sensitivities, specificities, and predictive values ranged from good to poor depending on the method, drug, and evidence type. Certain drugs were often associated with specific evidence types. Acetaminophen was frequently found in combination with fentanyl. Fentanyl test strips gave good scores for detecting fentanyl; otherwise, in-house methods using handheld devices had poor performance scores with novel drugs and drugs diluted in mixtures. The results showed that in-house testing of drug evidence has value for medical examiner overdose surveillance, but it is resource intensive, and success depends on collaboration with forensic laboratories.

A novel cgMLST for genomic surveillance of Yersinia enterocolitica infections in France allowed the detection and investigation of outbreaks in 2017-2021.

Enteric yersiniosis, the third most common food-borne zoonosis in Europe, is mainly caused by the pathogen Yersinia enterocolitica. In France, the yersiniosis microbiological surveillance is conducted at the Yersinia National Reference Laboratory (YNRL). Since 2017, isolates have been characterized by whole genome sequencing (WGS) followed by a 500-gene Yersinia-cgMLST. We report here the data of the WGS-based surveillance on Y. enterocolitica isolates for the 2017-2021 period. The YNRL characterized 7,642 Y. enterocolitica strains distributed in 2,497 non-pathogenic isolates from lineages 1Aa and 1Ab, and 5,145 specimens belonging to 8 pathogenic lineages. Among pathogenic isolates, lineage 4 was the most common (87.2%) followed by lineages 2/3-9b (10.6%), 2/3-5a (1.2%), 2/3-9a (0.6%), 3-3b, 3-3c, 1B, and 3-3d (0.1% per each). Importantly, we developed a routine surveillance system based on a new typing method consisting of a 1,727-genes core genome Multilocus Sequence Typing (cgMLST) specific to the species Y. enterocolitica followed by isolate clustering. Thresholds of allelic distances (AD) were determined and fixed for the clustering of isolates: AD ≤ 5 for lineages 4, 2/3-5a, and 2/3-9a, and AD ≤ 3 for lineage 2/3-9b. Clustering programs were implemented in 2019 in routine surveillance to detect genomic clusters of pathogenic isolates. In total, 419 clusters with at least 2 isolates were identified, representing 2,504 of the 3,503 isolates characterized between 2019 and 2021. Most clusters (n = 325) comprised 2 to 5 isolates. The new typing method proved to be useful for the molecular investigation of unusual grouping of cases as well as for the detection of genomic clusters in routine surveillance. IMPORTANCE: We describe here the new typing method used for molecular surveillance of Yersinia enterocolitica infections in France based on a novel core genome Multilocus Sequence Typing (cgMLST) specific to Y. enterocolitica species. This method can reliably identify the pathogenic Y. enterocolitica subspecies and compare the isolates with a high discriminatory power. Between 2017 and 2021, 5,145 pathogenic isolates belonging to 8 lineages were characterized and lineage 4 was by far the most common followed by lineage 2/3-9b. A clustering program was implemented, and detection thresholds were cross-validated by the molecular and epidemiological investigation of three unusual groups of Y. enterocolitica infections. The routine molecular surveillance system has been able to detect genomic clusters, leading to epidemiological investigations.

Advancing human genotyping: The Infinium HTS iSelect Custom microarray panel (Rita) development study.

Single Nucleotide Polymorphisms (SNPs), as the most prevalent type of variation in the human genome, play a pivotal role in influencing human traits. They are extensively utilized in diverse fields such as population genetics, forensic science, and genetic medicine. This study focuses on the 'Rita' BeadChip, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel facilitates the analysis of over 4000 markers efficiently and cost-effectively. After careful clustering performed on a set of 1000 samples, an evaluation of the Rita panel was undertaken, assessing its sensitivity, repeatability, reproducibility, precision, accuracy, and resistance to contamination. The panel's performance was evaluated in various scenarios, including sex estimation and parental relationship assessment, using GenomeStudio data analysis software. Findings show that over 95 % of the custom BeadChip assay markers were successful, with better performance of transitions over other mutations, and a considerably lower success rate for Y chromosome loci. An exceptional call rate exceeding 99 % was demonstrated for control samples, even with DNA input as low as 0.781 ng. Call rates above 80 % were still obtained with DNA quantities under 0.1 ng, indicating high sensitivity and suitability for forensic applications where DNA quantity is often limited. Repeatability, reproducibility, and precision studies revealed consistency of the panel's performance across different batches and operators, with no significant deviations in call rates or genotyping results. Accuracy assessments, involving comparison with multiple available genetic databases, including the 1000 Genome Project and HapMap, denoted over 99 % concordance, establishing the Rita panel's reliability in genotyping. The contamination study revealed insights into background noise and allowed the definition of thresholds for sample quality evaluation. Multiple metrics for differentiating between negative controls and true samples were highlighted, increasing the reliability of the obtained results. The sex estimation tool in GenomeStudio proved highly effective, correctly assigning sex in all samples with autosomal loci call rates above 97 %. The parental relationship assessment of family trios highlighted the utility of GenomeStudio in identifying genotyping errors or potential Mendelian inconsistencies, promoting the application of arrays such as Rita in kinship testing. Overall, this evaluation confirms the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications. With its custom content and adaptable design, it not only meets current genotyping demands but also opens avenues for further research and application expansion in the field of genetic analysis.