Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review.

BACKGROUND: Whole-genome sequencing (WGS) has been used widely to elucidate transmission of SARS-CoV-2 in acute healthcare settings, and to guide infection, prevention, and control (IPC) responses. AIM: To systematically appraise available literature, published between January 1st, 2020 and June 30th, 2022, describing the implementation of WGS in acute healthcare settings to characterize nosocomial SARS-CoV-2 transmission. METHODS: Searches of the PubMed, Embase, Ovid MEDLINE, EBSCO MEDLINE, and Cochrane Library databases identified studies in English reporting the use of WGS to investigate SARS-CoV-2 transmission in acute healthcare environments. Publications involved data collected up to December 31st, 2021, and findings were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. FINDINGS: In all, 3088 non-duplicate records were retrieved; 97 met inclusion criteria, involving 62 outbreak analyses and 35 genomic surveillance studies. No publications from low-income countries were identified. In 87/97 (90%), WGS supported hypotheses for nosocomial transmission, while in 46 out of 97 (47%) suspected transmission events were excluded. An IPC intervention was attributed to the use of WGS in 18 out of 97 (18%); however, only three (3%) studies reported turnaround times ≤7 days facilitating near real-time IPC action, and none reported an impact on the incidence of nosocomial COVID-19 attributable to WGS. CONCLUSION: WGS can elucidate transmission of SARS-CoV-2 in acute healthcare settings to enhance epidemiological investigations. However, evidence was not identified to support sequencing as an intervention to reduce the incidence of SARS-CoV-2 in hospital or to alter the trajectory of active outbreaks.

Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing.

AIM: To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS). METHODS: SARS-CoV-2 was detected by reverse transcriptase real-time polymerase chain reaction on viral RNA extracted from nasopharyngeal swabs. WGS was performed using an Oxford MinION Mk1C instrument following the ARTIC v3 sequencing protocol. High-quality consensus genomes were assembled with the artic-ncov2019 bioinformatics pipeline and viral phylogenetic trees were built, inferred by maximum-likelihood. Clusters were defined using a threshold of 0-1 single nucleotide polymorphisms (SNPs) between epidemiologically linked sequences. RESULTS: In April 2021, outbreaks of COVID-19 were declared on two wards at University Hospital Limerick after 4 healthcare-associated SARS-CoV-2 infections were detected by post-admission surveillance testing. Contact tracing identified 12 further connected cases; all with direct or indirect links to the ED 'COVID Zone'. All sequences were assigned to the Pangolin B.1.1.7 lineage by WGS, and SNP-level analysis revealed two distinct but simultaneous clusters of infections. Repeated transmission in the ED was demonstrated, involving patients accommodated on trolleys in crowded areas, resulting in multiple generations of infections across three inpatient hospital wards and subsequently to the local community. These findings informed mitigation efforts to prevent cross-transmission in the ED. CONCLUSION: Cross-transmission of SARS-CoV-2 occurred repeatedly in an overcrowded emergency department. Viral WGS elucidated complex viral transmission networks in our hospital and informed infection, prevention and control practice.

Clinical risk prediction model for 30-day all-cause re-hospitalisation or mortality in patients hospitalised with heart failure.

BACKGROUND: This study aimed to develop a risk prediction model (AUS-HF model) for 30-day all-cause re-hospitalisation or death among patients admitted with acute heart failure (HF) to inform follow-up after hospitalisation. The model uses routinely collected measures at point of care. METHODS: We analyzed pooled individual-level data from two cohort studies on acute HF patients followed for 30-days after discharge in 17 hospitals in Victoria, Australia (2014-2017). A set of 58 candidate predictors, commonly recorded in electronic medical records (EMR) including demographic, medical and social measures were considered. We used backward stepwise selection and LASSO for model development, bootstrap for internal validation, C-statistic for discrimination, and calibration slopes and plots for model calibration. RESULTS: The analysis included 1380 patients, 42.1% female, median age 78.7 years (interquartile range = 16.2), 60.0% experienced previous hospitalisation for HF and 333 (24.1%) were re-hospitalised or died within 30 days post-discharge. The final risk model included 10 variables (admission: eGFR, and prescription of anticoagulants and thiazide diuretics; discharge: length of stay>3 days, systolic BP, heart rate, sodium level (<135 mmol/L), >10 prescribed medications, prescription of angiotensin converting enzyme inhibitors or angiotensin receptor blockers, and anticoagulants prescription. The discrimination of the model was moderate (C-statistic = 0.684, 95%CI 0.653, 0.716; optimism estimate = 0.062) with good calibration. CONCLUSIONS: The AUS-HF model incorporating routinely collected point-of-care data from EMRs enables real-time risk estimation and can be easily implemented by clinicians. It can predict with moderate accuracy risk of 30-day hospitalisation or mortality and inform decisions around the intensity of follow-up after hospital discharge.

Indirect impact of rotavirus vaccination on viral causes of acute gastroenteritis in the elderly.

BACKGROUND: Rotavirus is considered a childhood infection causing acute gastroenteritis however, it also causes disease in adults which may be underestimated due to less frequent testing in this age-group. OBJECTIVES: To determine if paediatric rotavirus vaccination, introduced into Ireland in December 2016, affected the viral aetiology in those aged ≥65 yrs presenting with gastroenteritis in the pre- and post-vaccination years. Additionally, rotavirus genotypes in this age-group will be described. METHODS: Faecal samples from 2015 to 2019 for the investigation of gastroenteritis were tested by real-time (RT-) PCR for norovirus, adenovirus, rotavirus, Rotarix, astrovirus and sapovirus. Rotaviruses were genotyped by multiplex real-time RT-PCR or hemi-nested RT-PCR and a proportion confirmed by sequencing. RESULTS: 22,593 samples from adults aged ≥65 yrs were tested and 2566 (11 %) had ≥1 virus detected. Of 2566 positive samples, norovirus was detected in 82 %, rotavirus 9 %, sapovirus 6 %, astrovirus 3 % and adenovirus 1 %. Rotavirus and norovirus infections decreased between pre and post-vaccine year groups p < 0.001, whereas sapovirus, astrovirus and adenovirus remained unchanged. Between 2015-16 and 2018-19, G2P[4] increased and G4P[8] decreased, p < 0.001. In 2015-2019 there were 37 rotavirus outbreaks. Five geriatric outbreaks were genotyped and caused by G4P[8] (n = 1), G1P[8] (n = 1), G2P[4] (n = 2) and G12P[8] (n = 1). CONCLUSION: Rotavirus causes acute gastroenteritis in older people. Paediatric vaccination may have contributed to a decline in infections in the elderly; nevertheless, rotavirus continued to circulate in older people following vaccine introduction. Genotype distribution changed between the pre- and post-vaccine era however genotypes in outbreak and endemic settings were comparable.

Spontaneous Escherichia coli Meningitis and Pyogenic Ventriculitis in an Adult Receiving Anti-Tumour Necrosis Factor Alpha Therapy.

Presentation A 60-year-old male taking etanercept for ankylosing spondylitis was admitted to hospital with confusion and reduced level of consciousness over the preceding 24 hours. Diagnosis Magnetic Resonance Imaging (MRI) of his brain revealed pyogenic ventriculitis, and Escherichia coli was cultured from CSF. Treatment He required placement of an external ventricular drain and was treated with a prolonged course of intravenous ceftriaxone. Conclusion To our knowledge, this is the first reported case of spontaneous Gram-negative bacillary meningitis in a patient on anti-tumour necrosis factor (TNF)-alpha therapy, highlighting the risk of rare but serious infections associated with this class of medication.

The Heart Failure with Preserved Ejection Fraction Conundrum-Redefining the Problem and Finding Common Ground?

PURPOSE OF REVIEW: Heart failure with preserved ejection fraction (HFpEF) or diastolic heart failure (DHF) makes up more than half of all congestive heart failure presentations (CHF). With an ageing population, the case load and the financial burden is projected to increase, even to epidemic proportions. CHF hospitalizations add too much of the financial and infrastructure strain. Unlike systolic heart failure (SHF), much is still either uncertain or unknown. Specifically, in epidemiology, the disease burden is established; however, risk factors and pathophysiological associations are less clear; diagnostic tools are based on rigid parameters without the ability to accurately monitor treatments effects and disease progression; finally, therapeutics are similar to SHF but without prognostic data for efficacy. RECENT FINDINGS: The last several years have seen guidelines changing to account for greater epidemiological observations. Most of these remain general observation of shortness of breath symptom matched to static echocardiographic parameters. The introduction of exercise diastolic stress test has been welcome and warrants greater focus. HFpEF is likely to see new thinking in the coming decades. This review provides some of perspective on this topic.

Antifungal stewardship in critical care: Implementing a diagnostics-driven care pathway in the management of invasive candidiasis.

BACKGROUND: Invasive candidiasis (IC) is the most common invasive fungal disease in patients admitted to critical care and is associated with high mortality rates. Diagnosis can be delayed by the poor sensitivity of culture-based methods, leading to unnecessary use of empirical antifungal therapy (EAFT). The fungal biomarker (1-3)-ß-d-glucan (BDG) has been shown to aid in the diagnosis of IC in critical care and has been incorporated into antifungal stewardship (AFS) programmes. AIM: To describe our experience using a diagnostics-driven AFS programme incorporating the fungal biomarker BDG, analyse its impact on antifungal therapy (AFT), and gain an improved understanding of the epidemiology of IC in our critical care unit (CrCU). METHODS: An AFS care pathway incorporating BDG was introduced in the CrCU in St James's Hospital, Dublin. Following an educational programme, compliance with the pathway was prospectively audited between December 1st, 2017 and July 31st, 2018. RESULTS AND CONCLUSION: One hundred and nine AFT episodes were included, of which 95 (87%) had a BDG sent. Of those with BDG results available at the time of decision-making, 38 (63%) were managed in accordance with the care pathway. In compliant episodes without IC, median EAFT duration was 5.5 days [IQR 4-7] and no increase in mortality or subsequent IC was observed. Although adopting a diagnostics-driven approach was found to be useful in the cohort of patients with BDG results available, the use of once-weekly BDG testing did not result in an observed reduction in the consumption of anidulafungin, highlighting an important limitation of this approach.

Harmonizing analytical chemistry and clinical epidemiology for human biomonitoring studies. A case-study of plastic product chemicals in urine.

There is an interdisciplinary interface between analytical chemistry and epidemiology studies with respect to the design, execution, and analysis of environmental epidemiology cohorts and studies. Extracting meaningful results linking chemical exposure to human health outcomes begins at study design and spans the entire workflow. Here we discuss analytical experimental design from an exposure science perspective, and propose a reporting checklist for the design of human biomonitoring studies. We explain key analytical chemistry concepts of blanks and limits of reporting and present a case series of plastic product chemical exposure in prenatal urine specimens from the Barwon Infant Study.

Confirming a beneficial effect of the six-minute walk test on exercise confidence in patients with heart failure.

BACKGROUND: Low confidence to exercise is a barrier to engaging in exercise in heart failure patients. Participating in low to moderate intensity exercise, such as the six-minute walk test, may increase exercise confidence. AIM: To compare the effects of a six-minute walk test with an educational control condition on exercise confidence in heart failure patients. METHODS: This was a prospective, quasi-experimental design whereby consecutive adult patients attending an out-patient heart failure clinic completed the Exercise Confidence Scale prior to and following involvement in the six-minute walk test or an educational control condition. RESULTS: Using a matched pairs, mixed model design (n=60; 87% male; Mage=58.87±13.16), we identified a significantly greater improvement in Total exercise confidence (F(1,54)=4.63, p=0.036, partial η2=0.079) and Running confidence (F(1,57)=4.21, p=0. 045, partial η2=0.069) following the six-minute walk test compared to the educational control condition. These benefits were also observed after adjustment for age, gender, functional class and depression. CONCLUSION: Heart failure patients who completed a six-minute walk test reported greater improvement in exercise confidence than those who read an educational booklet for 10 min. The findings suggest that the six-minute walk test may be used as a clinical tool to improve exercise confidence. Future research should test these results under randomized conditions and examine whether improvements in exercise confidence translate to greater engagement in exercise behavior.

Self-Care Interventions That Reduce Hospital Readmissions in Patients With Heart Failure; Towards the Identification of Change Agents.

Unplanned hospital readmissions are the most important, preventable cost in heart failure (HF) health economics. Current professional guidelines recommend that patient self-care is an important means by which to reduce this burden. Patients with HF should be engaged in their care such as by detecting, monitoring, and managing their symptoms. A variety of educational and behavioural interventions have been designed and implemented by health care providers to encourage and support patient self-care. Meta-analyses support the use of self-care interventions to improve patient self-care and reduce hospital readmissions; however, efficacy is variable. The aim of this review was to explore methods to achieve greater clarity and consistency in the development and reporting of self-care interventions to enable 'change agents' to be identified. We conclude that advancement in this field requires more explicit integration and reporting on the behaviour change theories that inform the design of self-care interventions and the selection of behaviour change techniques. The systematic application of validated checklists, such as the Theory Coding Scheme and the CALO-RE taxonomy, will improve the systematic testing and refinement of interventions to enable 'change agent/s' to be identified and optimised.

Movement Disorders and Syndromic Autism: A Systematic Review.

Movement disorders are reported in idiopathic autism but the extent to which comparable movement disorders are found in syndromic/co-morbid autism is unknown. A systematic search of Medline, Embase, PsychINFO and CINAHL on the prevalence of specific movement disorder in syndromic autism associated with specific genetic syndromes identified 16 papers, all relating to Angelman syndrome or Rett syndrome. Prevalence rates of 72.7-100% and 25.0-27.3% were reported for ataxia and tremor, respectively, in Angelman syndrome. In Rett syndrome, prevalence rates of 43.6-50% were reported for ataxia and 27.3-48.3% for tremor with additional reports of dystonia, rigidity and pyramidal signs. However, reliable assessment measures were rarely used and recruitment was often not described in sufficient detail.

Anatomical redistribution of endogenous copper in embryonic mice overexpressing SOD1.

Mutations in the copper (Cu)- and zinc (Zn)-binding metalloenzyme Cu/Zn-superoxide dismutase (SOD1) cause familial forms of amyotrophic lateral sclerosis (ALS), a fatal adult-onset neurodegenerative disorder of the central nervous system (CNS). Transgenic over-expression of mutant SOD1 produces a robust ALS-like phenotype in mice. Despite being ubiquitously expressed from the moment of conception, the mechanisms underlying the CNS-selective phenotype of mutant SOD1 expression remain poorly understood. We have previously shown that the physiological requirement for copper in SOD1 is unsatiated in the CNS of adult mice overexpressing mutant SOD1 and that suboptimal delivery of Cu to SOD1 in these mice progressively worsens with age. An age-related impediment to Cu availability may therefore contribute to the adult onset of disease in cases of ALS caused by mutant SOD1. Here, we have extended the age-related investigation of Cu in SOD1 overexpressing transgenic mice to the embryonic stage of development. We used the quantitative in situ elemental imaging method, laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), to assess the endogenous distribution of Cu, Zn and other endogenous elements (carbon, phosphorus, sulphur, magnesium, manganese and iron) in the embryonic day 14 (E14) embryos of transgenic mice overexpressing wild-type human SOD1 (hSOD1Wt) or mutant human SOD1 (hSOD1G37R). We show that in contrast to adult mice, SOD1 overexpression (both wild-type and mutant) is associated with an overt redistribution of Cu from the liver to the CNS during embryonic development. Also in contrast to adult mice, Zn redistribution to the CNS in response to SOD1 over-expression is relatively modest in embryonic mice, being limited to the brainstem. No other elemental changes between genotypes were observed. Our application of quantitative LA-ICP-MS in situ imaging details the first anatomical mapping of endogenous elements in embryonic mice. The observed redistribution of Cu from the liver to the CNS in response to SOD1 overexpression during embryogenesis indicates that the impediment of Cu delivery to SOD1, which is evident in adult mutant SOD1 overexpressing mice, only occurs at a later stage in life.

Attenuated behaviour in Cornelia de Lange and fragile X syndromes.

BACKGROUND: Catatonia-like presentations in people with autism have been increasingly recognised within research and diagnostic guidelines. The recently developed Attenuated Behaviour Questionnaire has identified that attenuated behaviour [autistic catatonia] is very prevalent in people with autism spectrum disorders (ASDs) and associated with repetitive behaviour. In the current study, we investigated attenuated behaviour within two genetic syndromes associated with ASD and examined ASD and repetitive behaviour as longitudinal predictors of attenuated behaviour. METHOD: The Attenuated Behaviour Questionnaire was completed by parents/carers of 33 individuals with Cornelia de Lange syndrome (CdLS) and 69 with fragile X syndrome (FXS). Information collected from the same informants 4 years previously was utilised to examine ASD and repetitive behaviour as predictors of later attenuated behaviour, controlling for age, gender and ability. RESULTS: Catatonia-like attenuated behaviour was reported for individuals with CdLS (30.3%) and FXS (11.6%). Slowed movement was more prevalent in people with CdLS. No other phenotypic differences were observed. Across the two groups, repetitive behaviour predicted the presence of attenuated behaviour 4 years later, after controlling for age, gender and ability. CONCLUSIONS: Attenuated behaviour can be identified in individuals with CdLS and FXS and may have an effect on both adaptive behaviour and quality of life. Repetitive behaviours predicted subsequent risk within both groups and should be assessed by services as part of a pro-active strategy of support.

Delivering precision antimicrobial therapy through closed-loop control systems.

Sub-optimal exposure to antimicrobial therapy is associated with poor patient outcomes and the development of antimicrobial resistance. Mechanisms for optimizing the concentration of a drug within the individual patient are under development. However, several barriers remain in realizing true individualization of therapy. These include problems with plasma drug sampling, availability of appropriate assays, and current mechanisms for dose adjustment. Biosensor technology offers a means of providing real-time monitoring of antimicrobials in a minimally invasive fashion. We report the potential for using microneedle biosensor technology as part of closed-loop control systems for the optimization of antimicrobial therapy in individual patients.

Zirconium arene triple-decker sandwich complexes: synthesis, electronic structure and bonding.

Reduction of a permethylpentalene zirconium(iv) chloride complex [η8-Pn*Zr(µ-Cl)3/2]2(µ-Cl)2Li·THFx with KC8 in benzene results in activation of the aromatic solvent to yield an "inverted sandwich" complex, [η8-Pn*Zr]2(µ-η6:η6-C6H6) (1). The reactions in toluene, cumene, o-xylene and m-xylene also yield analogous solvent activated triple-decker sandwich complexes, which have been structurally characterised by single-crystal X-ray diffraction. Edge energies in the Zr K-edge XANES spectra are not distinguishable between 1 and formally Zr(ii) and Zr(iv) reference compounds, suggesting a broad edge structure. DFT calculations best describe the bonding in 1 as highly covalent with frontier molecular orbitals showing almost equal contributions from benzene and the Zr-permethylpentalene fragments.

Symptoms of Autism Spectrum Disorder (ASD) in Individuals with Mucopolysaccharide Disease Type III (Sanfilippo Syndrome): A Systematic Review.

The prevalence of autism spectrum disorder (ASD) in many genetic disorders is well documented but not as yet in Mucopolysaccharidosis type III (MPS III). MPS III is a recessively inherited metabolic disorder and evidence suggests that symptoms of ASD present in MPS III. This systematic review examined the extant literature on the symptoms of ASD in MPS III and quality assessed a total of 16 studies. Results indicated that difficulties within speech, language and communication consistent with ASD were present in MPS III, whilst repetitive and restricted behaviours and interests were less widely reported. The presence of ASD-like symptoms can result in late diagnosis or misdiagnosis of MPS III and prevent opportunities for genetic counselling and the provision of treatments.

Whole-brain metallomic analysis of the common marmoset (Callithrix jacchus).

Despite the importance of transition metals for normal brain function, relatively little is known about the distribution of these elemental species across the different tissue compartments of the primate brain. In this study, we employed laser ablation-inductively coupled plasma-mass spectrometry on PFA-fixed brain sections obtained from two adult common marmosets. Concurrent cytoarchitectonic, myeloarchitectonic, and chemoarchitectonic measurements allowed for identification of the major neocortical, archaecortical, and subcortical divisions of the brain, and precise localisation of iron, manganese, and zinc concentrations within each division. Major findings across tissue compartments included: (1) differentiation of white matter tracts from grey matter based on manganese and zinc distribution; (2) high iron concentrations in the basal ganglia, cortex, and substantia nigra; (3) co-localization of high concentrations of iron and manganese in the primary sensory areas of the cerebral cortex; and (4) high manganese in the hippocampus. The marmoset has become a model species of choice for connectomic, aging, and transgenic studies in primates, and the application of metallomics to these disciplines has the potential to yield high translational and basic science value.

The nature and prevalence of catatonic symptoms in young people with autism.

BACKGROUND: A proportion of young people with autism are reported to show catatonic-like symptoms in adolescence. The aetiology and prevalence of such presentations is unknown but include a set of behaviours that can best be described as attenuated. METHOD: The current study empirically investigated the presence and nature of such attenuated behaviours in children and adolescents with autism using a newly developed 34-item third party report measure, the Attenuated Behaviour Questionnaire. Caregivers or parents of young people with autism reported on the presentation of symptoms via the online completion of the Attenuated Behaviour Questionnaire and two established clinical measures of repetitive behaviour and depression. RESULTS: Initial results indicate that the Attenuated Behaviour Questionnaire is a workable clinical measure in this population with a degree of discriminant validity with regard to catatonia. Attenuated behaviour indicative of catatonia was relatively common in young people with autism with up to 20.2% having an existing diagnosis of catatonia and evidence of a relationship between attenuated behaviours and measures of depression and repetitive and restricted behaviours. CONCLUSION: Catatonic symptoms are more prevalent in young people with autism than previously thought, and the Attenuated Behaviour Questionnaire has potential as a clinical and research tool.

Low psychological resilience is associated with depression in patients with cardiovascular disease.

BACKGROUND: Psychological resilience is associated with an improved capacity to cope with chronic health challenges such as cardiovascular disease. AIMS: The aim of this cross-sectional study was to examine the relationship between psychological resilience and symptoms of depression in a non-acute cardiac outpatient population. METHODS: A total of 419 adult cardiac outpatients (288 men; mean±SD age 66.26±14.04 years) attending cardiovascular clinics completed the Sense of Coherence (SOC13) scale as a measure of psychological resilience and the Cardiac Depression Scale (CDS26) prior to their consultation. RESULTS: The total SOC13 score (mean±SD 64.02±14.24, range 19-91) was within the moderate range. Older patients (⩾65 years) were significantly more resilient than those aged <65 ( p<0.01). Psychological resilience (SOC13) was negatively correlated with depression (CDS26) ( r=-0.79; p<0.001) and inversely associated with affective, cognitive and somatic symptoms of depression. Psychological resilience, particularly meaningfulness, accounted for more of the variance in affective features of depression than for somatic features. CONCLUSION: These findings show that low psychological resilience was related to depression in this cohort of cardiac outpatients, particularly affective symptoms such as anhedonia and hopelessness. The SOC13 scale offers a complementary measure of psychological status that could be used to monitor, and possibly predict, patient coping and response to treatment throughout the cardiovascular disease trajectory.