Using GWAS and Machine Learning to Identify and Predict Genetic Variants Associated with Foodborne Bacteria Phenotypic Traits.

One of the main challenges in food microbiology is to prevent the risk of outbreaks by avoiding the distribution of food contaminated by bacteria. This requires constant monitoring of the circulating strains throughout the food production chain. Bacterial genomes contain signatures of natural evolution and adaptive markers that can be exploited to better understand the behavior of pathogen in the food industry. The monitoring of foodborne strains can therefore be facilitated by the use of these genomic markers capable of rapidly providing essential information on isolated strains, such as the source of contamination, risk of illness, potential for biofilm formation, and tolerance or resistance to biocides. The increasing availability of large genome datasets is enhancing the understanding of the genetic basis of complex traits such as host adaptation, virulence, and persistence. Genome-wide association studies have shown very promising results in the discovery of genomic markers that can be integrated into rapid detection tools. In addition, machine learning has successfully predicted phenotypes and classified important traits. Genome-wide association and machine learning tools have therefore the potential to support decision-making circuits intending at reducing the burden of foodborne diseases. The aim of this chapter review is to provide knowledge on the use of these two methods in food microbiology and to recommend their use in the field.

Molecular characteristics, risk factors, and clinical outcomes of methicillin-resistant Staphylococcus aureus infections among critically ill pediatric patients in Shanghai, 2016-2021.

Objective: Methicillin-resistant Staphylococcus aureus (MRSA) infection in children has been on the rise, which poses a serious threat to their health and life in China. The purpose of this study was to determine the molecular characteristics, risk factors, and clinical outcomes of MRSA infections among critically ill pediatric patients. Methods: A retrospective case-control study was performed in the pediatric intensive care unit (PICU) of a tertiary university teaching hospital. All children infected with culture-positive S. aureus in the PICU between January 2016 and December 2021 were included. Univariate and multivariable logistic regression analyses were used to identify potential risk factors for MRSA infection and clinical outcomes of S. aureus infection. All S. aureus isolates were characterized based on antimicrobial resistance, multilocus sequence typing (MLST) and Staphylococcal protein A (spa) typing. Results: Of 3,974 patients admitted to the PICU, 280 were diagnosed with a S. aureus infection during the 6-year study period. Among them, 43.2% (121/280) were MRSA. All MRSA isolates showed significantly higher rates of resistance to penicillin, erythromycin, clindamycin and tetracycline than MSSA strains. The MRSA strains consisted of 45 spa types and 20 sequence types (STs) (20 clonal complexes), among which the most frequently represented were ST59-t437and ST398-t034. Multivariable logistic regression revealed vaginal delivery, respiratory failure, co-infection with a virus, C-reactive protein (CRP) > 8 mg/L as significant risk factors for MRSA infection. There was no significant difference in all-cause mortality during hospitalization between the MRSA group and the MSSA group. Furthermore, independent predictors for mortality in patients with S. aureus infections were the presence of hypoproteinemia, hematopathy, septic shock, respiratory failure, fever, and white blood cell (WBC) > 15.0 × 109/L. Conclusions: The study revealed a high proportion of MRSA infections among critically ill pediatric patients, and found significant risk factors for MRSA infection and poor prognosis of S. aureus infection. Methicillin resistance did not contribute to the mortality in the current study. These findings will provide evidence-based practices to make the strategies of prevention and rational use of antibiotics for pediatric patients with S. aureus infection in the ICU.

Integrating the Thrifty Genotype and Evolutionary Mismatch Hypotheses to understand variation in cardiometabolic disease risk.

More than 60 years ago, James Neel proposed the Thrifty Genotype Hypothesis to explain the widespread prevalence of type 2 diabetes in Western, industrial contexts. This hypothesis posits that variants linked to conservative energy usage and increased fat deposition would have been favored throughout human evolution due to the advantages they could provide during periods of resource limitation. However, in industrial environments, these variants instead produce an increased risk of obesity, metabolic syndrome, type 2 diabetes, and related health issues. This hypothesis has been popular and impactful, with thousands of citations, many ongoing debates, and several spin-off theories in biomedicine, evolutionary biology, and anthropology. However, despite great attention, the applicability and utility of the Thrifty Genotype Hypothesis (TGH) to modern human health remains, in our opinion, unresolved. To move research in this area forward, we first discuss the original formulation of the TGH and its critiques. Second, we trace the TGH to updated hypotheses that are currently at the forefront of the evolutionary medicine literature-namely, the Evolutionary Mismatch Hypothesis. Third, we lay out empirical predictions for updated hypotheses and evaluate them against the current literature. Finally, we discuss study designs that could be fruitful for filling current knowledge gaps; here, we focus on partnerships with subsistence-level groups undergoing lifestyle transitions, and we present data from an ongoing study with the Orang Asli of Malaysia to illustrate this point. Overall, we hope this synthesis will guide new empirical research aimed at understanding how the human evolutionary past interacts with our modern environments to influence cardiometabolic health.

Clinical and mutational signatures of CRB1-associated retinopathies: a multicentre study.

BACKGROUND: To delineate the clinical and mutational signatures of patients with CRB1-associated retinopathies. METHODS: This multicentre retrospective cohort study involved 40 patients with CRB1 mutations and 40 age-matched and gender-matched inherited retinal diseases (IRDs). The detailed phenotyping and genotyping characteristics and genotype‒phenotype correlations of the patients were analysed. RESULTS: The mean age of CRB1 cohort was 27.33±14.63 years. Results showed that yellowish geographic macular degeneration (66.67%), small white or yellow dots (65.6%), hyperopia (62.5%), abnormally laminated retina (61.61%), epiretinal membrane (60.6%) and nummular pigment deposits (50%) were the most common signatures in patients with CRB1 mutations. These clinical signatures were notably more prevalent among CRB1 patients than among individuals in other IRD group (p<0.001). Early-onset severe retinal dystrophy/Leber congenital amaurosis (EOSRD/LCA) patients are more likely to present these signatures than retinitis pigmentosa (RP) and macular dystrophy (MD) patients. Furthermore, a significant reduction in central foveal thickness coupled with pronounced thickening of the peripheral retina was observed more distinctly in patients with EOSRD/LCA (p<0.001). The choroidal thickness was not significantly altered compared to the normal controls, but was markedly reduced in the other IRD groups (p<0.001). 55 pathogenic variants were identified, 20 of which were novel. Null mutations were associated with EOSRD/LCA patients, and missense mutations were more prevalent in MD and RP patients. CONCLUSIONS: Key clinical and mutational signatures were demonstrated in this study, providing a comprehensive update on CRB1-associated retinopathies that will aid in diagnosis and lay the foundation for future therapeutic studies.

Genotypic variation in resource exchange, use, and production traits in the legume-rhizobia mutualism.

Mutualisms, reciprocally beneficial interactions between two or more species, are ubiquitous in nature. A common feature of mutualisms is extensive context-dependent variation in fitness outcomes. This context-dependency is hypothesized to stem from the environment's mediation of the relative costs and benefits associated with mutualisms. However, traits related to the exchange of goods and services in mutualisms have received little attention in comparison to net fitness outcomes. In this study, we quantified the contribution of host and symbiont genotypes to variation in resource exchange, use, and production traits measured in the host using the model mutualism between legumes and nitrogen-fixing rhizobia. We predicted that plant genotype × rhizobia genotype (G × G) effects would be common to resource exchange traits because resource exchange is hypothesized to be governed by both interacting partners through bargaining. On the other hand, we predicted that plant genotype effects would dominate host resource use and production traits because these traits are only indirectly related to the exchange of resources. Consistent with our prediction for resource exchange traits, but not our prediction for resource use and production traits, we found that rhizobia genotype and G × G effects were the most common sources of variation in the traits that we measured. The results of this study complement the commonly observed phenomenon of G × G effects for fitness by showing that numerous mutualism traits also exhibit G × G variation. Furthermore, our results highlight the possibility that the exchange of resources as well as how partners use and produce traded resources can influence the evolution of mutualistic interactions. Our study lays the groundwork for future work to explore the relationship between resource exchange, use and production traits and fitness (i.e., selection) to test the competing hypotheses proposed to explain the maintenance of fitness variation in mutualisms.

Genetic variants in BDNF (rs6265 and rs11030119) and stroke susceptibility: a case-control analysis in South India.

BACKGROUND: Stroke occurs when the blood supply to part of the cerebral cortex is blocked, depriving it of oxygen and glucose, leading to cell death. It is a multifactorial disorder influenced by genetic, vascular, and environmental factors. AIM: This study investigated the association between two polymorphisms of the brain-derived neurotrophic factor (BDNF) gene, rs6265 and rs11030119, and stroke risk in a South Indian population. SUBJECTS AND METHODS: The study included 163 stroke cases and 160 healthy controls. Genomic DNA was extracted, and genotyping of rs6265 and rs11030119 polymorphisms was done using ARMS-PCR. Allelic and genotype frequencies were calculated, and odds ratios (OR) with 95% confidence intervals (CI) were determined using SPSS version 21.0. RESULTS: The rs6265 polymorphism was significantly associated with stroke risk, with the GG genotype more frequent in controls (OR 1.79, 95% CI 1.05-1.76, p = 0.01). The rs11030119 polymorphism showed a positive association, with the AA genotype more prevalent in cases (OR 2.70, 95% CI 1.34-5.44, p = 0.003). CONCLUSION: This study suggests an association between BDNF polymorphisms (rs6265, rs11030119) and stroke risk in a South Indian population. Further research in larger populations is necessary to confirm these findings and explore the mechanisms involved.

Deciphering Growth Patterns in Korean Children With Sotos Syndrome Through the Development of a Disease-Specific Growth Chart.

BACKGROUND: Sotos syndrome (SS) is a rare disorder characterized by overgrowth, distinctive facial features, and intellectual disability that is primarily caused by NSD1 pathogenic variants or 5q35 microdeletions. METHODS: We retrospectively analyzed the clinical characteristics and 339 anthropometric measurements over an average of 4.3 years of follow-up in 57 Korean children with SS. Sex-specific percentile curves for height, weight, and head circumference were developed using a generalized additive model that included factors such as location, scale, and shape. RESULTS: Males with SS demonstrated higher height before the age of 12.0, greater weight before 10.0, and larger head circumference before 15.5 compared to age- and sex-matched controls. Females with SS displayed higher height before 17.0, greater weight before 10.5, and larger head circumference before 12.0 compared to controls. Bone age was advanced compared to chronological age in 40% of males and 8% of females at their last visit. The predicted and target adult heights were not significantly different between groups. In subgroup analysis, the intragenic variant group (n = 48) showed a higher mean standard deviation score of height and weight in males, and head circumference in females compared to the microdeletion group (n = 9). CONCLUSIONS: Korean children with genetically confirmed SS exhibited overgrowth in height, weight, and head circumference. Overgrowth phenotypes were more prominent in patients with NSD1 intragenic variants than in those with microdeletions. This is the first study to provide reference data on the growth of Korean children with SS.

Prevalence of Human Papillomavirus (HPV) Infection and its Association With Pap Smear Findings Among Women Attending a Gynecology Clinic in Khorasan Razavi-Iran.

BACKGROUND: Human papillomavirus (HPV) infection is the most common sexual transmitted disease and Pap smears and HPV testing are crucial for early detection. Advancements in HPV testing improve accuracy, but optimal screening strategies are still debated. This cross-sectional study explores HPV genotypes and predictors of infection among Iranian women undergoing gynecological screening. Study Design: A retrospective cross-sectional study. METHODS: Women undergoing their initial cervical screening enrolled in this study. Cervical cytology samples for Pap smear analysis were collected from women referred to the genetic laboratory of Academic Center for Education Culture and Research (ACECR), Khorasan Razavi, during gynecological visits, adhering to standardized liquid-based cytology protocols. These samples were obtained over a one-year period since January 2023. Statistical analyses were conducted using SPSS version 21.0, with a significance level set at P<0.05. RESULTS: A total of 328 women enrolled in this study. The mean age of participants was 36±11 years and the overall HPV prevalence was 37.5% (n=123). Among HPV-positive women, nearly half (48.7%) had a single HPV genotype. Genotypes 6 (13%), 16 (12.3%), and 53 (6.7%) were the most prevalent types. Notably, high-risk HPV genotypes (16 and 18 among all) were identified in one-fourth of the study population. Women with endocervical/transformation zone cells had 25% higher odds of having HPV infection, and having mild, moderate, and severe inflammation increased the odds of having HPV infection by 14%, 11%, and 20%, respectively. CONCLUSION: The considerably high prevalence of HPV infection highlights the significance of HPV prevention programs in this population. Neither bacterial vaginosis nor candida infection showed a direct link to HPV positivity.

Diversity, functional classification and genotyping of SHV ß-lactamases in Klebsiella pneumoniae.

Interpreting the phenotypes of bla SHV alleles in Klebsiella pneumoniae genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal bla SHV alleles or additional plasmid-borne bla SHV alleles that have extended-spectrum ß-lactamase (ESBL) activity and/or ß-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood. This has led to confusion in the literature and in antimicrobial resistance (AMR) gene databases [e.g. the National Center for Biotechnology Information (NCBI) Reference Gene Catalog and the ß-lactamase database (BLDB)] over the specific functionality of individual sulfhydryl variable (SHV) protein variants. Therefore, the identification of ESBL-producing strains from K. pneumoniae genome data is complicated. Here, we reviewed the experimental evidence for the expansion of SHV enzyme function associated with specific aa substitutions. We then systematically assigned SHV alleles to functional classes (WT, ESBL and BLI resistant) based on the presence of these mutations. This resulted in the re-classification of 37 SHV alleles compared with the current assignments in the NCBI's Reference Gene Catalog and/or BLDB (21 to WT, 12 to ESBL and 4 to BLI resistant). Phylogenetic and comparative genomic analyses support that (i) SHV-1 (encoded by bla SHV-1) is the ancestral chromosomal variant, (ii) ESBL- and BLI-resistant variants have evolved multiple times through parallel substitution mutations, (iii) ESBL variants are mostly mobilized to plasmids and (iv) BLI-resistant variants mostly result from mutations in chromosomal bla SHV. We used matched genome-phenotype data from the KlebNET-GSP AMR Genotype-Phenotype Group to identify 3999 K. pneumoniae isolates carrying one or more bla SHV alleles but no other acquired ß-lactamases to assess genotype-phenotype relationships for bla SHV. This collection includes human, animal and environmental isolates collected between 2001 and 2021 from 24 countries. Our analysis supports that mutations at Ambler sites 238 and 179 confer ESBL activity, whilst most omega-loop substitutions do not. Our data also provide support for the WT assignment of 67 protein variants, including 8 that were noted in public databases as ESBL. These eight variants were reclassified as WT because they lack ESBL-associated mutations, and our phenotype data support susceptibility to third-generation cephalosporins (SHV-27, SHV-38, SHV-40, SHV-41, SHV-42, SHV-65, SHV-164 and SHV-187). The approach and results outlined here have been implemented in Kleborate v2.4.1 (a software tool for genotyping K. pneumoniae), whereby known and novel bla SHV alleles are classified based on causative mutations. Kleborate v2.4.1 was updated to include ten novel protein variants from the KlebNET-GSP dataset and all alleles in public databases as of November 2023. This study demonstrates the power of sharing AMR phenotypes alongside genome data to improve the understanding of resistance mechanisms.

A plant mutant screen CURE integrated with core biology concepts showed effectiveness in course design and students' perceived learning gains.

Course-based undergraduate research experiences (CUREs) provide students with valuable opportunities to engage in research in a classroom setting, expanding access to research opportunities for undergraduates, fostering inclusive research and learning environments, and bridging the gap between the research and education communities. While scientific practices, integral to the scientific discovery process, have been widely implemented in CUREs, there have been relatively few reports emphasizing the incorporation of core biology concepts into CURE curricula. In this study, we present a CURE that integrates core biology concepts, including genetic information flow, phenotype-genotype relationships, mutations and mutants, and structure-function relationships, within the context of mutant screening and gene loci identification. The design of this laboratory course aligns with key CURE criteria, as demonstrated by data collected through the laboratory course assessment survey (LCAS). The survey of undergraduate research experiences (SURE) demonstrates students' learning gains in both course-directed skills and transferrable skills following their participation in the CURE. Additionally, concept survey data reflect students' self-perceived understanding of the aforementioned core biological concepts. Given that genetic mutant screens are central to the study of gene function in biology, we anticipate that this CURE holds potential value for educators and researchers who are interested in designing and implementing a mutant screen CURE in their classrooms. This can be accomplished through independent research or by establishing partnerships between different units or institutions.

Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities.

Associations with soil microorganisms are crucial for plants' overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here, we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 genotypes of cultivated sunflower (Helianthus annuus) at 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial, and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial, and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen Sclerotinia were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.IMPORTANCEDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial, and fungal communities are driven primarily by site soil and climatic differences, but genotype can interact with site to influence the composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen Sclerotinia sclerotiorum were widespread but significantly affected by site, while a subset was also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial, and fungal community assembly and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.

[Selection of pharmacogenomic variants and methodology for their use in community pharmacy]. / Selección de variantes farmacogenómicas y metodología para su uso en farmacia comunitaria.

Regulatory agencies such as the Food and Drug Administration (FDA) and the European Medicines Agency (EMA) recognize pharmacogenetics as a key tool in their pharmacological guidelines for pharmaceutical counseling. In this context, community pharmacies play a crucial role in addressing this healthcare need, which could lead to a significant improvement in patients' quality of life by preventing ineffective or contraindicated treatments.In this work, we conducted a systematic review of the available scientific evidence regarding druggene interactions relevant to community pharmacy. We identified the main genes and polymorphisms associated with treatment response and adverse effects in primary care. Finally, we propose a model for implementing pharmacogenetic services in community pharmacies.

Role of total polyphenol content in seed germination characteristics of spring barley varieties amidst climate change.

The amount of total polyphenol content (TPC) in the grain could provide insights into the conditions during maturation and might also serve as an indicator of the grain's ability to germinate in the malting process or as seeds in the field. Varieties with higher natural TPC content might exhibit better germination parameters both in the field and in the malt house. This study investigates the relationship between TPC and seed germination characteristics i.e. seed vigour in four spring barley varieties over two years, considering diverse environmental conditions and exposure to drought conditions. The evaluation of seed germination characteristics in barley, with a focus on the root length and average diameter under drought conditions (-0.5 MPa) and suboptimal temperature (10 °C), was conducted. Drought conditions were induced using polyethylene glycol (PEG 6000). After durations of seven and fourteen days, the germinated seeds from the Petri dishes were scanned and subjected to analysis using WinRHIZO software following the metrics: Len 7, Len 14 (root length after seven and fourteen days in cm) and AvgD 7, AvgD 14 (root diameter after seven and fourteen days in mm). The findings support our initial hypothesis, indicating a variety-specific relationship between seed germination characteristics and increased TPC, where higher germination parameters might be associated with elevated TPC levels in some barley varieties.

Exploring the impact of plant genotype and fungicide treatment on endophytic communities in tomato stems.

This study examines how plant genotype can influence the microbiome by comparing six tomato genotypes (Solanum lycopersicum) based on their traditional vs. commercial backgrounds. Using Illumina-based sequencing of the V6-V8 regions of 16S and ITS2 rRNA genes, we analyzed and compared the endophytic bacterial and fungal communities in stems to understand how microbiota can differ and be altered in plant genotypes and the relation to human manipulation. Our results reflect that traditional genotypes harbor significantly more exclusive microbial taxa and a broader phylogenetic background than the commercial ones. Traditional genotypes were significantly richer in Eurotiomycetes and Sordariomycetes fungi, while Lasiosphaeriaceae was more prevalent in commercial genotypes. TH-30 exhibited the highest bacterial abundance, significantly more than commercial genotypes, particularly in Actinomycetia, Bacteroidia, and Gammaproteobacteria. Additionally, traditional genotypes had higher bacterial diversity, notably in orders like Cytophagales, Xanthomonadales, and Burkholderiales. Moreover, we performed an evaluation of the impact of a systemic fungicide (tebuconazole-dichlofluanide) to simulate a common agronomic practice and determined that a single fungicide treatment altered the stem endophytic microbiota. Control plants had a higher prevalence of fungal orders Pleosporales, Helotiales, and Glomerellales, while treated plants were dominated by Sordariomycetes and Laboulbeniomycetes. Fungal community diversity significantly decreased, but no significant impact was observed on bacterial diversity. Our study provides evidence that the background of the tomato variety impacts the fungal and bacterial stem endophytes. Furthermore, these findings suggest the potential benefits of using of traditional genotypes as a source of novel beneficial microbiota that may prove highly valuable in unpredicted challenges and the advancement in sustainable agriculture.

Genotype x environment interaction and yield stability of soybean (Glycine max l.) genotypes in multi-environment trials (METs) in Nigeria.

Genotype × environment interaction (GEI) poses a critical challenge to plant breeders by complicating the identification of stable variety (ies) for performance across diverse environments. GGE biplot and AMMI analyses have been identified as the most effective and appropriate statistical techniques for identifying stable and high-performing genotypes across diverse environments. The objective of this study was to identify widely adapted and high-yielding soybean genotypes from Multi-Locational Trials (MLTs) using GGE and AMMI biplot analyses. Fifteen IITA-bred elite soybean lines and three standard checks were evaluated for stability of performance in a 3 × 6 alpha lattice design with three replications across seven locations in Nigeria. Significant (p < 0.001) differences were detected among genotypes, environments, and GEI for grain yield, which ranged between 979.8 kg ha-1 and 3645 kg ha-1 with a mean of 2324 kg ha-1. To assess the stability of genotypes, analyses were conducted using the general linear method, GGE, and the Additive Main Effect and Multiplicative Interaction (AMMI) approach, as well as WAAS and ASV rank indices. In the GGE biplot model, the first two principal components accounted for 67.4 % of the total variation, while in the AMMI model, the first two Interaction Principal Component Axes (IPCA1 and IPCA2) explained 73.20 % and 11.40 % of the variation attributed to genotype by environment interaction, respectively. GGE biplot identified G10 and G16 as the most stable and productive genotypes, while WAASB index revealed G16, G10, G9, G4 and G2 as the most adaptive, stable and productive genotypes across locations, and ASV identified G9, G13, G4, G14 and G10 as the most stable and productive. Consequently, genotypes G2, G4, G9, G10 and G16 displayed outstanding and stable grain yield performance across the test locations and are, therefore, recommended for release as new soybean varieties suitable for cultivation in the respective mega environment where they performed best. More importantly, the two genotypes are recommended for recycling as sources of high-yield and yield stability genes, and as parental lines for high-yield and stable performance for future breeding and genomic selection.

A rare case of keratitis due to co-infection with Plectosphaerella cucumerina and Acanthamoeba T5 genotype.

Aims: This report summarizes clinical findings, diagnosis, management, and long term outcomes of a recalcitrant Plectosphaerella and Acanthamoeba keratitis. Methods and materials: An otherwise healthy male patient presented with a corneal infiltrate with predominantly fungal characteristics, but atypical in terms of progression. The infiltrate remained undiagnosed even after several scrapings, and aqueous tap cultures. Since conventional therapy with antifungals and intrastromal voriconazole injections was ineffective, a therapeutic keratoplasty was done. Results: The excised corneal button was cultured; molecular identification of the Acanthamoeba and fungus isolates revealed the rare T5 genotype and the even rarer Plectosphaerella cucumerina. Judicious use of antifungals and anti-amoebic drops in the post-operative period, combined with gradual introduction of steroids resulted in favourable visual outcome. Conclusions: The T5 is the second most frequent environmental Acanthamoeba, but rarely isolated clinically. Plectosphaerella keratitis has been reported only 4 times in the literature. Neither of these have been previously reported from India.

Cocirculation of Newcastle Disease Virus Genotypes XII and VII Along with Nonvirulent Forms Characterized in Domestic Birds from Peru.

Newcastle disease virus (NDV) is one of the most important pathogens affecting poultry, given its impact on health and production systems worldwide, despite widespread vaccination. Over the past 20 years, NDV has caused severe outbreaks of disease in Peru. These outbreaks primarily affected gamecocks and broiler chickens, with an additional reported case in commercial layers. Therefore, our objective was to identify and characterize the virus responsible for these cases in Peru. We analyzed 14 suspected clinical cases in domestic birds for NDV detection, isolation, and genetic characterization. Among these cases, seven involved gamecocks, with six genotype XII isolates and one genotype VII isolate, representing the first report of NDV genotype VII isolate from fighting roosters in Peru. Additionally, among the six cases in broiler chickens, we detected four genotype XII isolates and three genotype II isolates, including one sample containing both genotypes XII and II. Furthermore, a genotype I viral isolate was identified in a laying hen. Hence, we concluded that two divergent, highly virulent NDV genotypes, genotypes XII and VII, along with avirulent forms such as genotypes I and II are circulating among domestic birds in Peru. Genetic analysis indicates that these viruses are evolving locally within avian species and offers the basis necessary for vaccine adaptation to circulating viruses. Our results highlight the cocirculation of multiple virulent and nonvirulent NDV genotypes in domestic birds in Peru, underscoring the potential role of gamecocks as a viral source of virulent NDV strains in the country and the occurrence of outbreaks in poultry farms.

Cocirculación de los genotipos XII y VII del virus de la enfermedad de Newcastle junto con formas no virulentas caracterizadas en aves domésticas del Perú. El virus de la enfermedad de Newcastle (NDV) es uno de los patógenos más importantes que afectan a la avicultura, dado su impacto en la salud y los sistemas de producción en todo el mundo, a pesar de la vacunación generalizada. Durante los últimos 20 años, el virus de la enfermedad de Newcastle ha causado graves brotes de enfermedades en el Perú. Estos brotes afectaron principalmente a gallos de pelea y pollos de engorde, con un caso adicional reportado en aves de postura comerciales. Por lo tanto, nuestro objetivo fue identificar y caracterizar el virus responsable de estos casos en el Perú. Se analizaron 14 casos cl'inicos sospechosos en aves domésticas para la detección, aislamiento y caracterización genética del virus de Newcastle. Entre estos casos, siete involucraron gallos de pelea, con seis aislamientos del genotipo XII y un aislado del genotipo VII, lo que representa el primer informe de aislamiento del genotipo VII del virus de Newcastle de gallos de pelea en Perú. Además, entre los seis casos en pollos de engorde, se detectaron cuatro aislados del genotipo XII y tres aislados del genotipo II, incluida una muestra que con-ten'ia ambos genotipos XII y II. Además, se identificó un aislado viral de genotipo I en una gallina de postura. Por lo tanto, se concluye que dos genotipos divergentes y altamente virulentos del virus de Newcastle, los genotipos XII y VII, junto con formas avirulentas como los genotipos I y II, están circulando entre las aves domésticas en el Perú. El análisis genético indica que estos virus están evolucionando localmente dentro de las especies aviares y ofrece las bases necesarias para realizar adaptaciones de las vacunas contra los virus circulantes. Nuestros resultados resaltan la cocirculación de múltiples genotipos del virus de Newcastle virulentos y no virulentos en aves domésticas en Perú, subrayando el papel potencial de los gallos de pelea como fuente viral de cepas virulentas del virus de Newcastle en el pa'is y la aparición de brotes en granjas av'icolas.

A randomised controlled trial to determine the effect of genotype-based personalised diet and physical activity advice for FTO genotype (rs9939609) delivered via email on healthy eating motivation in young adults.

The prevalence of obesity continues to rise, and public health dietary recommendations are not being adhered to. The transition to higher education is a period of risk for weight gain in young adults and has been demonstrated as a good time to initiate behaviour change. A genotype-based personalised approach to dietary recommendations may motivate young adults to maintain or adopt positive dietary behaviours. The aim of the present study was to determine the efficacy of genotype-based personalised dietary and physical activity advice on healthy eating motivation in young adults. Participants were young adults (n = 153), aged 18-25 years. Baseline measures (participant characteristics, height, weight, body mass index [BMI], body fat percentage [BF%], healthy eating motivation and physical activity) were collected. Participants were genotyped for a SNP in the FTO gene (rs99396090) and randomly allocated (stratified for genotype) to three different groups (1. Genotype-based personalised advice: dietary and physical activity advice based on genotype, BMI and reported physical activity; 2. Non-genotype-based personalised advice: dietary and physical activity advice based on BMI and reported physical activity; 3. Control: no advice). A week after receipt of advice delivered via email, participants completed the healthy eating motivation questionnaire for a second time. Genotype-based personalised dietary advice did not affect healthy eating motivation: when participants were analysed across the whole group (p = 0.417), when analysed according to those informed of a risk or non-risk-associated genotype (p = 0.287), or when analysed according to those with a BMI (>25 kg/m2; p = 0.336) or BF% (male >18%, female >31%; p = 0.387) outside the healthy range. There was also no significant difference in healthy eating motivation at 1-week in the control or non-genotype-based advice groups. Genotype-based personalised advice for the prevention of obesity did not affect healthy eating motivation in this group of healthy, young adults.

Ethnic diversity in Chilean blood groups: A comprehensive analysis of genotypes, phenotypes, alleles and the immunogenic potential of antigens in northern, southern and central regions.

BACKGROUND AND OBJECTIVES: The available information on blood groups in the Chilean population is derived from studies on aboriginal cohorts and routine serological test results. The purpose of this study is to conduct a comprehensive analysis of genotypes, phenotypes and blood group alleles in donors from northern, central and southern Chile using molecular methods. MATERIALS AND METHODS: Overall, 850 samples from donors in northern, central and southern Chile were genotyped. Allelic, genotypic and antigenic frequencies were calculated and compared among regions. Of these, 602 samples were analysed by haemagglutination, and discrepancies found between phenotypes and genotypes were investigated. The immunogenic potential of antigens was calculated by the Giblett equation, using the antigenic frequencies of donors from Santiago and the alloantibody frequencies of patients from the same region. RESULTS: Alleles of low prevalence, variant alleles and those responsible for the absence of high-prevalence antigens were found. Significant differences were observed between the antigenic frequencies of the three regions. Discrepancies between serologic and molecular results were mostly attributed to the molecular background affecting antigen expression. In the calculation of the immunogenic potential of antigens, the highest value was attributed to the Dia antigen. CONCLUSION: These findings represent the first molecular characterization of blood group antigens in Chileans. Our results highlight the necessity of using molecular tools to explore the genotypes underlying variant phenotypes, low-frequency antigens and antigens lacking specific antisera that cannot be detected by haemagglutination. Additionally, they emphasize the importance of understanding the distribution of blood groups among different populations.