Imputation of single nucleotide polymorphism genotypes in ungenotyped sport horses from the genotypes of their progeny.

Many sport horse studbooks worldwide use microsatellite markers for parentage verification. However, many have expressed a desire to introduce genomic selection using genome-wide dense single nucleotide polymorphism (SNP) genotypes to complement their current breeding programmes. Hence, it does not make sense to genotype the same animal for both microsatellite markers and SNP markers. Transitioning to SNP-based parentage verification is an obvious solution but one barrier to this transition is the lack of SNP data on parents from which to verify parentage against. Therefore, the objective of this study was to assess the ability to impute the SNP genotype of a stallion from the genotypes of its progeny, with or without the consideration of the genotype of the progeny's dam. Genotype information from 55 935 SNPs was available on 13 327 horses. A total of 98 stallions had genotype data on 10 progeny and the genotypes of these stallions were used as a test population. Genome-wide genotype imputation was undertaken by combining a family- and population-based imputation approach. Several different scenarios were assessed to quantify the ability to accurately impute the genotype of a stallion based on genotype data of incrementally more half-sibling progeny. Using genomic information from four progeny the average genotype concordance of the imputed sire genotype compared to the actual sire's genotype was 0.932. The average genotype concordance rate increased to 0.960 when the genotypes of 10 progeny were included in the imputation process. The inclusion of the genotypes of the dams of the progeny improved the concordance rate from 0.932 to 0.977 when based on the genotype of just four progeny and their dams and from 0.960 to 0.996 when based on the genotype of 10 progeny and their dams. These results suggest it is possible to impute the genotype of a non-genotyped horse from the genotypes of its progeny and that the inclusion of the genotypes of the dams of the progeny improves this imputation accuracy further.

Protracted transmission and persistence of ST80 vancomycin-resistant Enterococcus faecium clonal complex types CT2933, CT2932 and CT1916 in a large Irish hospital: a 39-month whole-genome sequencing study.

BACKGROUND: Vancomycin-resistant Enterococcus faecium (VREfm) are significant nosocomial pathogens. Sequence type (ST) 80 vanA-encoding VREfm predominate in Irish hospitals, but their transmission is poorly understood. AIMS: To investigate transmission and persistence of predominant complex type (CT) VREfm in two wards of an Irish hospital (H1) using whole-genome sequencing, and their intra- and inter-hospital dissemination. METHODS: Rectal screening (N = 330, September 2019 to December 2022) and environmental (N = 48, November 2022 to December 2022) E. faecium were investigated. Isolate relatedness was assessed by core-genome multi-locus sequence typing (cgMLST) and core-genome single nucleotide polymorphism (cgSNP) analysis. Likely transmission chains were identified using SeqTrack (https://graphsnp.fordelab.com/graphsnp) using cgSNP data and recovery location. Well-characterized E. faecium (N = 908) from seven Irish hospitals including H1 (June 2017 to July 2022) were also investigated. FINDINGS: Conventional MLST assigned isolates to nine STs (ST80, 82%). cgMLST identified three predominant ST80 CTs (CT2933, CT2932 and CT1916) (55% of isolates) of related isolates (≤20 allelic differences). cgSNP analysis differentiated these CTs into multiple distinct closely related genomic clusters (≤10 cgSNPs). Parisimonious network construction identified 55 likely inter- and intra-ward transmissions with epidemiological support between patients ≤30 days involving 73 isolates (≤10 cgSNPs) from seven genomic clusters. Numerous other likely transmissions over longer time periods without evident epidemiological links were identified, suggesting persistence and unidentified reservoirs contribute to dissemination. The three CTs predominated among E. faecium (N = 1286) in seven hospitals, highlighting inter-hospital spread without known epidemiological links. CONCLUSION: This study revealed the long-term intra- and inter-hospital dominance of three major CT ST80 VREfm lineages, widespread transmission and persistence, implicating unidentified reservoirs.

Localising terrestrially derived pollution inputs to threatened near-shore coral reefs through stable isotope, water quality and oceanographic analysis.

Near-shore coral reefs are at high-risk of exposure to pollution from terrestrial activities. Pollution impacts can vary with site-specific factors that span sources, rainfall and oceanographic characteristics. To effectively manage pollution, we need to understand how these factors interact. In this study, we detect terrestrially derived nutrient inputs on near-shore reefs at Norfolk Island, South Pacific by analysis of dissolved inorganic nitrogen (DIN) and stable isotopes. When compared to a reef site with predominantly oceanic inputs, we found that both the lagoon and a small reef adjacent to a catchment have signatures of human-derived DIN shown through depleted δ15N signatures in macroalgae. We find pollution exposure of reef sites is associated with known and unknown sources, rainfall and mixing of water with the open ocean. In characterising exposure of reef sites we highlight the role of site-specific context in influencing pollution exposure for benthic communities even in remote island systems.

Arbuscular mycorrhizal fungi improve the growth and disease resistance of the invasive plant Wedelia trilobata.

AIMS: Arbuscular mycorrhizal fungi (AMF) are symbiotic partners of many invasive plants, however, it is still unclear how AMF contribute to traits that are important for the successful invasion of their host and how environmental factors, such as nutrient conditions, influence this. This study was to explore the effects of Glomus versiforme (GV) and Glomus mosseae (GM) on the growth and disease resistance of the invasive plant Wedelia trilobata under different nutrient conditions. METHODS AND RESULTS: We found that GV and GM had higher root colonization rates resulting in faster W. trilobata growth under both low-N and low-P nutrient conditions compared to the normal condition. Also, the colonization of W. trilobata by GV significantly reduced the infection area of the pathogenic fungus Rhizoctonia solani under low-N conditions. CONCLUSIONS: These results demonstrated that AMF can promote the growth and pathogenic defence of W. trilobata in a nutrient-poor environment, which might contribute to their successful invasion into certain type of habitats. SIGNIFICANCE AND IMPACT OF THE STUDY: In this study, we report for the first time that AMF can promote growth and disease resistance of W. trilobata under nutrient-poor environment, which contribute to a better understanding of plant invasion.

Hospital outbreak of linezolid-resistant and vancomycin-resistant ST80 Enterococcus faecium harbouring an optrA-encoding conjugative plasmid investigated by whole-genome sequencing.

BACKGROUND: Linezolid is an antibiotic used to treat infections caused by multi-drug-resistant Gram-positive bacteria. Linezolid resistance in enterococci has been reported with increasing frequency, with a recent rise in resistance encoded by optrA, poxtA or cfr. AIM: To investigate a hospital outbreak of linezolid- and vancomycin-resistant Enterococcus faecium (LVREfm) using whole-genome sequencing (WGS). METHODS: Thirty-nine VREfm from patient screening (19 isolates, 17 patients) and environmental sites (20 isolates) recovered in October 2019 were investigated. Isolates were screened using polymerase chain reaction for optrA, poxtA and cfr, and underwent Illumina MiSeq WGS. Isolate relatedness was assessed using E. faecium core genome multi-locus sequence typing (cgMLST). One LVREfm underwent MinION long-read WGS (Oxford Nanopore Technologies) and hybrid assembly with MiSeq short-read sequences to resolve an optrA-encoding plasmid. FINDINGS: Twenty isolates (51.3%) were LVREfm and optrA-positive, including the LVREfm from the index patient. A closely related cluster of 28 sequence type (ST) 80 isolates was identified by cgMLST, including all 20 LVREfm and eight linezolid-susceptible VREfm, with an average allelic difference of two (range 0-10), indicating an outbreak. Nineteen (95%) LVREfm harboured a 56,684-bp conjugative plasmid (pEfmO_03). The remaining LVREfm exhibited 44.1% sequence coverage to pEfmO_03. The presence of pEfmO_03 in LVREfm and the close relatedness of the outbreak cluster isolates indicated the spread of a single strain. The outbreak was terminated by enhanced infection prevention and control (IPC) and environmental cleaning measures, ceasing ward admissions and ward-dedicated staff. CONCLUSION: WGS was central in investigating an outbreak of ST80 LVREfm. The rapid implementation of enhanced IPC measures terminated the outbreak.

Doctor-Patient Communication in an Outpatient Setting

Aim To evaluate doctor patient communication within gynaecological oncology services in Ireland. Methods An anonymous and confidential 20 question survey was designed by the patient advocacy group ISGOPPI and distributed in three gynaecological oncology outpatient clinics in tertiary referral centres. Results A total of 84 patients completed the survey in the 3 Dublin hospitals. Doctors surveyed ranged from senior house officer to consultant level. Overall women were very satisfied with the communication they had received from their doctor. 85% felt that they the doctor listened to them and took their opinion into account. 84% of patients felt that the doctor's body language was appropriate throughout the consultation. One of the main issues for women surveyed was waiting times. 33% of women waited over an hour to see their doctor and over 30% of women did not receive contact details of the clinical nurse specialist. Conclusion Overall our study shows that patients in gynae-oncology clinics are satisfied with the communication from their doctors. The main issues for patients were waiting times and contact details for follow up questions.

Research trends in equine movement analysis, future opportunities and potential barriers in the digital age: A scoping review from 1978 to 2018.

BACKGROUND: Since Muybridge's 'horse in motion', researchers in the equine movement analysis field continue to improve objective analysis and performance monitoring while ensuring representative data capture. However, subjective evaluation remains the primary method of equine gait analysis in the applied setting, despite evidence highlighting the unreliability of this approach. OBJECTIVES: To map research trends, limitations and opportunities across the diverse equine gait analysis literature. STUDY DESIGN: Joanna Briggs Institute and Cochrane systematic scoping review. METHODS: Search terms were chosen based on the 'PICO' framework and included keywords such as: Equine, Gait, Kinematics and Analysis. Studies were excluded based on predetermined criteria by two independent researchers. Data were extracted from 510 articles from 1978 to 2018. RESULTS: Insights derived from movement analysis appear to be driven by tool availability. Observational research (42.9%) was the most popular study design. Use of wearable technology as a primary research tool is established within the field, accounting for 13.5% of studies. Analysis of limitations identified 17.8% of studies citing challenges to the transferability of research results. Restricted sample size appears to be an underlying contributor to many of the limitations identified. In terms of research opportunities, advances in intervention studies were called for (10.4% of studies) in the following three areas; clinical, rehabilitative exercise and performance/training. MAIN LIMITATIONS: This review was confined to research in the English language. CONCLUSIONS: Standardised research reporting may alleviate sample size issues by facilitating data pooling, database creation and meta-analyses. Large holistic data collections and application frameworks based on wearable technologies are not reflected in the current equine gait analysis literature and thus represent an interesting opportunity for this field. Progress and lessons learned from the human field of movement analysis can be useful in supporting this potential development.

Identifying avoidable switchboard delays in England's NHS hospitals: phase one of the national SWITCH project.

BACKGROUND: Inter-hospital communication frequently requires mediation via a switchboard. Identifying and eliminating switchboard inefficiencies may improve patient care. METHODS: All 175 acute hospital switchboards in England were contacted six times. Call contents and duration were recorded. No clinician calls or bleeps were connected. RESULTS: The mean delay before contacting a switchboard operative was 55±46 seconds. 115 hospitals (66%) used automated switchboards; 34 of these (30%) had infection control messages. Robot operators introduced an additional 40 second delay versus humans (mean 70.3±28 versus 29.8±23 seconds, p<0.0001). Multivariate analysis identified robot operators (HR 5.1, p<0.0001) and infection control messages (HR 2.9, p=0.003) as predictors of delays over 60 seconds. CONCLUSIONS: There are significant avoidable delays in contacting switchboard operatives across England. Quality improvement is underway.

Population pharmacokinetics of teicoplanin and attainment of pharmacokinetic/pharmacodynamic targets in adult patients with haematological malignancy.

OBJECTIVES: To describe the population pharmacokinetics of teicoplanin in adult patients with haematological malignancies receiving higher than standard doses, and to perform Monte Carlo simulations to determine dosing regimens associated with optimal teicoplanin concentrations. METHODS: This was a hospital-based clinical trial (EudraCT 2013-004535-72). Nine blood samples were collected on Day 3, plus single trough samples on Days 7 and 10, and 24 and 48 hours after the last dose. Teicoplanin minimum inhibitory concentrations were determined for Gram-positive isolates from study patients. Population pharmacokinetic analyses and Monte Carlo dosing simulations were undertaken using Pmetrics. RESULTS: Thirty adult haematological malignancy patients were recruited with a mean (SD) loading dose, age, total body weight, and creatinine clearance of 9.5 (1.9) mg/kg, 63 (12) years, 69.1 (15.8) kg, and 72 (41) mL/min, respectively. A three-compartment linear pharmacokinetic model best described the teicoplanin concentration data. Covariates supported for inclusion in the final model were creatinine clearance for clearance and total body weight for volume of the central compartment. The median (IQR) area under the concentration-time curve from 48 to 72 hours (AUC48-72h) was 679 (319) mg.h/L. There was a strong correlation between the AUC48-72h and trough concentration at 72 hours (Pearson correlation coefficient 0.957, p <0.001). Dosing simulations showed that administration of five loading doses at 12-hourly intervals, stratified by total body weight and creatinine clearance, increased the probability of achieving target concentrations within 72 hours. CONCLUSIONS: To increase the number of patients achieving optimal teicoplanin concentrations an individualized dosing approach, based on body weight and creatinine clearance, is recommended.

Prevalence of liver fluke infection in Irish horses and assessment of a serological test for diagnosis of equine fasciolosis.

BACKGROUND: There is little information on the prevalence of Fasciola hepatica infection in the horse population in Ireland or the potential impact of fluke infection on animal health. OBJECTIVES: To investigate F. hepatica infection in the Irish horse population and to assess the diagnostic potential of an indirect enzyme-linked immunosorbent assay (ELISA) based on the F. hepatica recombinant cathepsin L1 (CL1) antigen. STUDY DESIGN: Cross-sectional abattoir survey of horses for liver fluke status. METHODS: Animals (n = 200) were examined at an abattoir between May 2013 and April 2014. Horses were graded ante mortem for body condition score. Blood and faeces were collected and livers were examined post mortem by gross morphology. A cohort (n = 35) of livers were also examined histologically. Haematology and blood biochemistry, including serum liver enzyme activities, were measured and faeces were sedimented for egg counts. Serum was assayed by indirect ELISA using a recombinant CL1. RESULTS: The prevalence of liver fluke infection was 9.5%. There was no correlation between liver fluke status and time of year, breed classification, age group, sex, body condition score, ante mortem assessment, strongyle infection status, serum liver enzyme activities or CL1 concentration. A comparison of the CL1 ELISA in horse sera compared with a reference standard diagnosis showed high specificity of 95.6% (95% confidence interval [CI] 91.5-98.0%), but low sensitivity of 42.1% (95% CI 20.2-66.5%). MAIN LIMITATIONS: This study is limited by its nature as an abattoir study, the relatively small number of animals examined (n = 200), and the absence of a known negative group of horses. CONCLUSIONS: Blood biomarkers are not good indicators of liver fluke infection and the CL1 ELISA is not a sensitive tool for diagnosis of fluke infection in the horse. The prevalence of F. hepatica in horses indicates that further research is required to assess the potential impact of liver fluke on equine liver health.

The relationship between magical thinking, inferential confusion and obsessive-compulsive symptoms.

Inferential confusion is an under-researched faulty reasoning process in obsessive-compulsive disorder (OCD). Based on an overreliance on imagined possibilities, it shares similarities with the extensively researched construct of thought-action fusion (TAF). While TAF has been proposed as a specific subset of the broader construct of magical thinking, the relationship between inferential confusion and magical thinking is unexplored. The present study investigated this relationship, and hypothesised that magical thinking would partially mediate the relationship between inferential confusion and obsessive-compulsive symptoms. A non-clinical sample of 201 participants (M = 34.94, SD = 15.88) were recruited via convenience sampling. Regression analyses found the hypothesised mediating relationship was supported, as magical thinking did partially mediate the relationship between inferential confusion and OC symptoms. Interestingly, inferential confusion had the stronger relationship with OC symptoms in comparison to the other predictor variables. Results suggest that inferential confusion can both directly and indirectly (via magical thinking) impact on OC symptoms. Future studies with clinical samples should further investigate these constructs to determine whether similar patterns emerge, as this may eventually inform which cognitive errors to target in treatment of OCD.

Interspecific patterns of phenotypic selection do not predict intraspecific patterns.

We estimated linear (ß) and nonlinear (γ) selection gradients to quantify host plant-mediated selection on the trait gall size in each of 22 unequally sampled subpopulations of the cynipid gall wasp Belonocnema treatae. We characterized the relationship between variation in subpopulation sample size and the magnitude of and the variance among selection gradients. We then tested the hypothesis that the intraspecific patterns we observed would follow two patterns that have emerged from published estimates of linear and nonlinear selection gradients compiled across species, namely that the average magnitude of ß and γ and the variance among estimated ß and γ decrease with increasing sample size. For both ß and γ, intraspecific patterns of phenotypic selection in relation to sample size were not predicted by interspecific patterns. Thus, our results suggest that when selection is heterogeneous among subpopulations, variation in the biological basis for selection is more important in influencing estimates of selection than is variation in study size. Our study highlights the value of inspecting selection in relation to sampling effort at the level at which understanding the sources of variation in selection is most important, among populations within species.

DNA-based species detection capabilities using laser transmission spectroscopy.

Early detection of invasive species is critical for effective biocontrol to mitigate potential ecological and economic damage. Laser transmission spectroscopy (LTS) is a powerful solution offering real-time, DNA-based species detection in the field. LTS can measure the size, shape and number of nanoparticles in a solution and was used here to detect size shifts resulting from hybridization of the polymerase chain reaction product to nanoparticles functionalized with species-specific oligonucleotide probes or with the species-specific oligonucleotide probes alone. We carried out a series of DNA detection experiments using the invasive freshwater quagga mussel (Dreissena bugensis) to evaluate the capability of the LTS platform for invasive species detection. Specifically, we tested LTS sensitivity to (i) DNA concentrations of a single target species, (ii) the presence of a target species within a mixed sample of other closely related species, (iii) species-specific functionalized nanoparticles versus species-specific oligonucleotide probes alone, and (iv) amplified DNA fragments versus unamplified genomic DNA. We demonstrate that LTS is a highly sensitive technique for rapid target species detection, with detection limits in the picomolar range, capable of successful identification in multispecies samples containing target and non-target species DNA. These results indicate that the LTS DNA detection platform will be useful for field application of target species. Additionally, we find that LTS detection is effective with species-specific oligonucleotide tags alone or when they are attached to polystyrene nanobeads and with both amplified and unamplified DNA, indicating that the technique may also have versatility for broader applications.

Summary of an NIH workshop to identify research needs to improve the monitoring of iodine status in the United States and to inform the DRI.

The Office of Dietary Supplements (ODS) at the NIH sponsored a workshop on May 12-13, 2011, to bring together representatives from various NIH institutes and centers as a first step in developing an NIH iodine research initiative. The workshop also provided an opportunity to identify research needs that would inform the dietary reference intakes for iodine, which were last revised in 2001. Iodine is required throughout the life cycle, but pregnant women and infants are the populations most at risk of deficiency, because iodine is required for normal brain development and growth. The CDC monitors iodine status of the population on a regular basis, but the status of the most vulnerable populations remains uncertain. The NIH funds very little investigator-initiated research relevant to iodine and human nutrition, but the ODS has worked for several years with a number of other U.S. government agencies to develop many of the resources needed to conduct iodine research of high quality (e.g., validated analytical methods and reference materials for multiple types of samples). Iodine experts, scientists from several U.S. government agencies, and NIH representatives met for 2 d to identify iodine research needs appropriate to the NIH mission.

Postmating isolation and genetically variable host use in ecologically divergent host forms of Neochlamisus bebbianae leaf beetles.

Ecological speciation studies have more thoroughly addressed premating than postmating reproductive isolation. This study examines multiple postmating barriers between host forms of Neochlamisus bebbianae leaf beetles that specialize on Acer and Salix trees. We demonstrate cryptic isolation and reduced hybrid fitness via controlled matings of these host forms. These findings reveal host-associated postmating isolation, although a nonecological, 'intrinsic' basis for these patterns cannot be ruled out. Host preference and performance results among cross types further suggest sex-linked maternal effects on these traits, whereas family effects indicate their genetic basis and associated variation. Genes of major effect appear to influence these traits. Together with previous findings of premating isolation and adaptive differentiation in sympatry, our results meet many assumptions of 'speciation with gene flow' models. Here, such gene flow is likely asymmetric, with consequences for the dynamics of future ecological divergence and potential ecological speciation of these host forms.

Mutation detection rate and spectrum in familial hypercholesterolaemia patients in the UK pilot cascade project.

Cascade testing using DNA-mutation information is now recommended in the UK for patients with familial hypercholesterolaemia (FH). We compared the detection rate and mutation spectrum in FH patients with a clinical diagnosis of definite (DFH) and possible (PFH) FH. Six hundred and thirty-five probands from six UK centres were tested for 18 low-density lipoprotein receptor gene (LDLR) mutations, APOB p.Arg3527Gln and PCSK9 p.Asp374Tyr using a commercial amplification refractory mutation system (ARMS) kit. Samples with no mutation detected were screened in all exons by single strand conformation polymorphism analysis (SSCP)/denaturing high performance liquid chromatography electrophoresis (dHPLC)/direct-sequencing, followed by multiplex ligation-dependent probe amplification (MLPA) to detect deletions and duplications in LDLR.The detection rate was significantly higher in the 190 DFH patients compared to the 394 PFH patients (56.3% and 28.4%, p > 0.00001). Fifty-one patients had inadequate information to determine PFH/DFH status, and in this group the detection rate was similar to the PFH group (25.5%, p = 0.63 vs PFH). Overall, 232 patients had detected mutations (107 different; 6.9% not previously reported). The ARMS kit detected 100 (44%) and the MLPA kit 11 (4.7%). Twenty-eight (12%) of the patients had the APOB p.Arg3527Gln and four (1.7%) had the PCSK9 p.Asp374Tyr mutation. Of the 296 relatives tested from 100 families, a mutation was identified in 56.1%. In 31 patients of Indian/Asian origin 10 mutations (two previously unreported) were identified. The utility of the ARMS kit was confirmed, but sequencing is still required in a comprehensive diagnostic service for FH. Even in subjects with a low clinical suspicion of FH, and in those of Indian origin, mutation testing has an acceptable detection rate.