DNA hypomethylation silences anti-tumor immune genes in early prostate cancer and CTCs.

Cancer is characterized by hypomethylation-associated silencing of large chromatin domains, whose contribution to tumorigenesis is uncertain. Through high-resolution genome-wide single-cell DNA methylation sequencing, we identify 40 core domains that are uniformly hypomethylated from the earliest detectable stages of prostate malignancy through metastatic circulating tumor cells (CTCs). Nested among these repressive domains are smaller loci with preserved methylation that escape silencing and are enriched for cell proliferation genes. Transcriptionally silenced genes within the core hypomethylated domains are enriched for immune-related genes; prominent among these is a single gene cluster harboring all five CD1 genes that present lipid antigens to NKT cells and four IFI16-related interferon-inducible genes implicated in innate immunity. The re-expression of CD1 or IFI16 murine orthologs in immuno-competent mice abrogates tumorigenesis, accompanied by the activation of anti-tumor immunity. Thus, early epigenetic changes may shape tumorigenesis, targeting co-located genes within defined chromosomal loci. Hypomethylation domains are detectable in blood specimens enriched for CTCs.

Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis.

Circulating tumor cell clusters (CTC clusters) are present in the blood of patients with cancer but their contribution to metastasis is not well defined. Using mouse models with tagged mammary tumors, we demonstrate that CTC clusters arise from oligoclonal tumor cell groupings and not from intravascular aggregation events. Although rare in the circulation compared with single CTCs, CTC clusters have 23- to 50-fold increased metastatic potential. In patients with breast cancer, single-cell resolution RNA sequencing of CTC clusters and single CTCs, matched within individual blood samples, identifies the cell junction component plakoglobin as highly differentially expressed. In mouse models, knockdown of plakoglobin abrogates CTC cluster formation and suppresses lung metastases. In breast cancer patients, both abundance of CTC clusters and high tumor plakoglobin levels denote adverse outcomes. Thus, CTC clusters are derived from multicellular groupings of primary tumor cells held together through plakoglobin-dependent intercellular adhesion, and though rare, they greatly contribute to the metastatic spread of cancer.

The burden and dynamics of hospital-acquired SARS-CoV-2 in England.

Hospital-based transmission had a dominant role in Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV) epidemics1,2, but large-scale studies of its role in the SARS-CoV-2 pandemic are lacking. Such transmission risks spreading the virus to the most vulnerable individuals and can have wider-scale impacts through hospital-community interactions. Using data from acute hospitals in England, we quantify within-hospital transmission, evaluate likely pathways of spread and factors associated with heightened transmission risk, and explore the wider dynamical consequences. We estimate that between June 2020 and March 2021 between 95,000 and 167,000 inpatients acquired SARS-CoV-2 in hospitals (1% to 2% of all hospital admissions in this period). Analysis of time series data provided evidence that patients who themselves acquired SARS-CoV-2 infection in hospital were the main sources of transmission to other patients. Increased transmission to inpatients was associated with hospitals having fewer single rooms and lower heated volume per bed. Moreover, we show that reducing hospital transmission could substantially enhance the efficiency of punctuated lockdown measures in suppressing community transmission. These findings reveal the previously unrecognized scale of hospital transmission, have direct implications for targeting of hospital control measures and highlight the need to design hospitals better equipped to limit the transmission of future high-consequence pathogens.

NR4A1 regulates expression of immediate early genes, suppressing replication stress in cancer.

Deregulation of oncogenic signals in cancer triggers replication stress. Immediate early genes (IEGs) are rapidly and transiently expressed following stressful signals, contributing to an integrated response. Here, we find that the orphan nuclear receptor NR4A1 localizes across the gene body and 3' UTR of IEGs, where it inhibits transcriptional elongation by RNA Pol II, generating R-loops and accessible chromatin domains. Acute replication stress causes immediate dissociation of NR4A1 and a burst of transcriptionally poised IEG expression. Ectopic expression of NR4A1 enhances tumorigenesis by breast cancer cells, while its deletion leads to massive chromosomal instability and proliferative failure, driven by deregulated expression of its IEG target, FOS. Approximately half of breast and other primary cancers exhibit accessible chromatin domains at IEG gene bodies, consistent with this stress-regulatory pathway. Cancers that have retained this mechanism in adapting to oncogenic replication stress may be dependent on NR4A1 for their proliferation.

Migratory birds modulate niche tradeoffs in rhythm with seasons and life history.

Movement is a key means by which animals cope with variable environments. As they move, animals construct individual niches composed of the environmental conditions they experience. Niche axes may vary over time and covary with one another as animals make tradeoffs between competing needs. Seasonal migration is expected to produce substantial niche variation as animals move to keep pace with major life history phases and fluctuations in environmental conditions. Here, we apply a time-ordered principal component analysis to examine dynamic niche variance and covariance across the annual cycle for four species of migratory crane: common crane (Grus grus, n = 20), demoiselle crane (Anthropoides virgo, n = 66), black-necked crane (Grus nigricollis, n = 9), and white-naped crane (Grus vipio, n = 9). We consider four key niche components known to be important to aspects of crane natural history: enhanced vegetation index (resources availability), temperature (thermoregulation), crop proportion (preferred foraging habitat), and proximity to water (predator avoidance). All species showed a primary seasonal niche "rhythm" that dominated variance in niche components across the annual cycle. Secondary rhythms were linked to major species-specific life history phases (migration, breeding, and nonbreeding) as well as seasonal environmental patterns. Furthermore, we found that cranes' experiences of the environment emerge from time-dynamic tradeoffs among niche components. We suggest that our approach to estimating the environmental niche as a multidimensional and time-dynamical system of tradeoffs improves mechanistic understanding of organism-environment interactions.

Structural Transformations of Metal-Organic Cages through Tetrazine-Alkene Reactivity.

The assembly of metal-organic cages is governed by metal ion coordination preferences and the geometries of the typically rigid and planar precursor ligands. PdnL2n cages are among the most structurally diverse, with subtle differences in the metal-ligand coordination vectors resulting in drastically different assemblies, however almost all rely on rigid aromatic linkers to avoid the formation of intractable mixtures. Here we exploit the inverse electron-demand Diels-Alder (IEDDA) reaction between tetrazine linker groups and alkene reagents to trigger structural changes induced by post-assembly modification. The structure of the 1,4-dihydropyridazine produced by IEDDA (often an afterthought in click chemistry) is crucial; its two sp3 centers increase flexibility and nonplanarity, drastically changing the range of accessible coordination vectors. This triggers an initial Pd4L8 tetrahedral cage to transform into different Pd2L4 lantern cages, with both the transformation extent (thermodynamics) and rate (kinetics) dependent on the alkene dienophile selected. With cyclopentene, the unsymmetrical 1,4-dihydropyridazine ligands undergo integrative sorting in the solid state, with both head-to-tail orientation and enantiomer selection, leading to a single isomer from the 39 possible. This preference is rationalized through entropy, symmetry, and hydrogen bonding. Subsequent oxidation of the 1,4-dihydropyridazine to the aromatic pyridazine rigidifies the ligands, restoring planarity. The oxidized ligands no longer fit in the lantern structure, inducing further structural transformations into Pd4L8 tetrahedra and Pd3L6 double-walled triangles. The concept of controllable addition of limited additional flexibility and then its removal through well-defined reactivity we envisage being of great interest for structural transformations of any class of supramolecular architecture.

Antimicrobial resistance prevalence in bloodstream infection in 29 European countries by age and sex: An observational study.

BACKGROUND: Antibiotic usage, contact with high transmission healthcare settings as well as changes in immune system function all vary by a patient's age and sex. Yet, most analyses of antimicrobial resistance (AMR) ignore demographic indicators and provide only country-level resistance prevalence values. This study aimed to address this knowledge gap by quantifying how resistance prevalence and incidence of bloodstream infection (BSI) varied by age and sex across bacteria and antibiotics in Europe. METHODS AND FINDINGS: We used patient-level data collected as part of routine surveillance between 2015 and 2019 on BSIs in 29 European countries from the European Antimicrobial Resistance Surveillance Network (EARS-Net). A total of 6,862,577 susceptibility results from isolates with age, sex, and spatial information from 944,520 individuals were used to characterise resistance prevalence patterns for 38 different bacterial species and antibiotic combinations, and 47% of these susceptibility results were from females, with a similar age distribution in both sexes (mean of 66 years old). A total of 349,448 isolates from 2019 with age and sex metadata were used to calculate incidence. We fit Bayesian multilevel regression models by country, laboratory code, sex, age, and year of sample to quantify resistant prevalence and provide estimates of country-, bacteria-, and drug-family effect variation. We explore our results in greater depths for 2 of the most clinically important bacteria-antibiotic combinations (aminopenicillin resistance in Escherichia coli and methicillin resistance in Staphylococcus aureus) and present a simplifying indicative index of the difference in predicted resistance between old (aged 100) and young (aged 1). At the European level, we find distinct patterns in resistance prevalence by age. Trends often vary more within an antibiotic family, such as fluroquinolones, than within a bacterial species, such as Pseudomonas aeruginosa. Clear resistance increases by age for methicillin-resistant Staphylococcus aureus (MRSA) contrast with a peak in resistance to several antibiotics at approximately 30 years of age for P. aeruginosa. For most bacterial species, there was a u-shaped pattern of infection incidence with age, which was higher in males. An important exception was E. coli, for which there was an elevated incidence in females between the ages of 15 and 40. At the country-level, subnational differences account for a large amount of resistance variation (approximately 38%), and there are a range of functional forms for the associations between age and resistance prevalence. For MRSA, age trends were mostly positive, with 72% (n = 21) of countries seeing an increased resistance between males aged 1 and 100 years and a greater change in resistance in males. This compares to age trends for aminopenicillin resistance in E. coli which were mostly negative (males: 93% (n = 27) of countries see decreased resistance between those aged 1 and 100 years) with a smaller change in resistance in females. A change in resistance prevalence between those aged 1 and 100 years ranged up to 0.51 (median, 95% quantile of model simulated prevalence using posterior parameter ranges 0.48, 0.55 in males) for MRSA in one country but varied between 0.16 (95% quantile 0.12, 0.21 in females) to -0.27 (95% quantile -0.4, -0.15 in males) across individual countries for aminopenicillin resistance in E. coli. Limitations include potential bias due to the nature of routine surveillance and dependency of results on model structure. CONCLUSIONS: In this study, we found that the prevalence of resistance in BSIs in Europe varies substantially by bacteria and antibiotic over the age and sex of the patient shedding new light on gaps in our understanding of AMR epidemiology. Future work is needed to determine the drivers of these associations in order to more effectively target transmission and antibiotic stewardship interventions.

Altered expression of vesicular trafficking machinery in prostate cancer affects lysosomal dynamics and provides insight into the underlying biology and disease progression.

BACKGROUND: This study focuses on the role of lysosomal trafficking in prostate cancer, given the essential role of lysosomes in cellular homoeostasis. METHODS: Lysosomal motility was evaluated using confocal laser scanning microscopy of LAMP-1-transfected prostate cells and spot-tracking analysis. Expression of lysosomal trafficking machinery was evaluated in patient cohort databases and through immunohistochemistry on tumour samples. The roles of vesicular trafficking machinery were evaluated through over-expression and siRNA. The effects of R1881 treatment on lysosome vesicular trafficking was evaluated by RNA sequencing, protein quantification and fixed- and live-cell microscopy. RESULTS: Altered regulation of lysosomal trafficking genes/proteins was observed in prostate cancer tissue, with significant correlations for co-expression of vesicular trafficking machinery in Gleason patterns. The expression of trafficking machinery was associated with poorer patient outcomes. R1881 treatment induced changes in lysosomal distribution, number, and expression of lysosomal vesicular trafficking machinery in hormone-sensitive prostate cancer cells. Manipulation of genes involved in lysosomal trafficking events induced changes in lysosome positioning and cell phenotype, as well as differential effects on cell migration, in non-malignant and prostate cancer cells. CONCLUSIONS: These findings provide novel insights into the altered regulation and functional impact of lysosomal vesicular trafficking in prostate cancer pathogenesis.

Synthesis of Boron-Containing Nucleoside Analogs.

Over the last century, nucleoside-based therapeutics have demonstrated remarkable effectiveness in the treatment of a wide variety of diseases from cancer to HIV. In addition, boron-containing drugs have recently emerged as an exciting and fruitful avenue for medicinal therapies. However, borononucleosides have largely been unexplored in the context of medicinal applications. Herein, we report the synthesis, isolation, and characterization of two novel boron-containing nucleoside compound libraries which may find utility as therapeutic agents. Our synthetic strategy employs efficient one-step substitution reactions between a diverse variety of nucleoside scaffolds and an assortment of n-alkyl potassium trifluoroborate-containing electrophiles. We demonstrated that these alkylation reactions are compatible with cyclic and acyclic nucleoside substrates, as well as increasing alkyl chain lengths. Furthermore, regioselective control of product formation can be readily achieved through manipulation of base identity and reaction temperature conditions.

Implications of reducing antibiotic treatment duration for antimicrobial resistance in hospital settings: A modelling study and meta-analysis.

BACKGROUND: Reducing antibiotic treatment duration is a key component of hospital antibiotic stewardship interventions. However, its effectiveness in reducing antimicrobial resistance is uncertain and a clear theoretical rationale for the approach is lacking. In this study, we sought to gain a mechanistic understanding of the relation between antibiotic treatment duration and the prevalence of colonisation with antibiotic-resistant bacteria in hospitalised patients. METHODS AND FINDINGS: We constructed 3 stochastic mechanistic models that considered both between- and within-host dynamics of susceptible and resistant gram-negative bacteria, to identify circumstances under which shortening antibiotic duration would lead to reduced resistance carriage. In addition, we performed a meta-analysis of antibiotic treatment duration trials, which monitored resistant gram-negative bacteria carriage as an outcome. We searched MEDLINE and EMBASE for randomised controlled trials published from 1 January 2000 to 4 October 2022, which allocated participants to varying durations of systemic antibiotic treatments. Quality assessment was performed using the Cochrane risk-of-bias tool for randomised trials. The meta-analysis was performed using logistic regression. Duration of antibiotic treatment and time from administration of antibiotics to surveillance culture were included as independent variables. Both the mathematical modelling and meta-analysis suggested modest reductions in resistance carriage could be achieved by reducing antibiotic treatment duration. The models showed that shortening duration is most effective at reducing resistance carriage in high compared to low transmission settings. For treated individuals, shortening duration is most effective when resistant bacteria grow rapidly under antibiotic selection pressure and decline rapidly when stopping treatment. Importantly, under circumstances whereby administered antibiotics can suppress colonising bacteria, shortening antibiotic treatment may increase the carriage of a particular resistance phenotype. We identified 206 randomised trials, which investigated antibiotic duration. Of these, 5 reported resistant gram-negative bacteria carriage as an outcome and were included in the meta-analysis. The meta-analysis determined that a single additional antibiotic treatment day is associated with a 7% absolute increase in risk of resistance carriage (80% credible interval 3% to 11%). Interpretation of these estimates is limited by the low number of antibiotic duration trials that monitored carriage of resistant gram-negative bacteria, as an outcome, contributing to a large credible interval. CONCLUSIONS: In this study, we found both theoretical and empirical evidence that reducing antibiotic treatment duration can reduce resistance carriage, though the mechanistic models also highlighted circumstances under which reducing treatment duration can, perversely, increase resistance. Future antibiotic duration trials should monitor antibiotic-resistant bacteria colonisation as an outcome to better inform antibiotic stewardship policies.

Modeling the novel SERD elacestrant in cultured fulvestrant-refractory HR-positive breast circulating tumor cells.

PURPOSE: Metastatic hormone receptor-positive (HR+) breast cancer initially responds to serial courses of endocrine therapy, but ultimately becomes refractory. Elacestrant, a new generation FDA-approved oral selective estrogen receptor degrader (SERD) and antagonist, has demonstrated efficacy in a subset of women with advanced HR+breast cancer, but there are few patient-derived models to characterize its effect in advanced cancers with diverse treatment histories and acquired mutations. METHODS: We analyzed clinical outcomes with elacestrant, compared with endocrine therapy, among women who had previously been treated with a fulvestrant-containing regimen from the recent phase 3 EMERALD Study. We further modeled sensitivity to elacestrant, compared with the currently approved SERD, fulvestrant in patient-derived xenograft (PDX) models and cultured circulating tumor cells (CTCs). RESULTS: Analysis of the subset of breast cancer patients enrolled in the EMERALD study who had previously received a fulvestrant-containing regimen indicates that they had better progression-free survival with elacestrant than with standard-of-care endocrine therapy, a finding that was independent estrogen receptor (ESR1) gene mutations. We modeled elacestrant responsiveness using patient-derived xenograft (PDX) models and in ex vivo cultured CTCs derived from patients with HR+breast cancer extensively treated with multiple endocrine therapies, including fulvestrant. Both CTCs and PDX models are refractory to fulvestrant but sensitive to elacestrant, independent of mutations in ESR1 and Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha (PIK3CA) genes. CONCLUSION: Elacestrant retains efficacy in breast cancer cells that have acquired resistance to currently available ER targeting therapies. Elacestrant may be an option for patients with HR+/HER2- breast cancer whose disease progressed on fulvestrant in the metastatic setting. TRANSLATIONAL RELEVANCE: Serial endocrine therapy is the mainstay of management for metastatic HR+breast cancer, but acquisition of drug resistance highlights the need for better therapies. Elacestrant is a recently FDA-approved novel oral selective estrogen receptor degrader (SERD), with demonstrated efficacy in the EMERALD phase 3 clinical trial of refractory HR+breast cancer. Subgroup analysis of the EMERALD clinical trial identifies clinical benefit with elacestrant in patients who had received prior fulvestrant independent of the mutational status of the ESR1 gene, supporting its potential utility in treating refractory HR+breast cancer. Here, we use pre-clinical models, including ex vivo cultures of circulating tumor cells and patient-derived xenografts, to demonstrate the efficacy of elacestrant in breast cancer cells with acquired resistance to fulvestrant.

Phonon Signatures in Photon Correlations.

We show that the second-order, two-time correlation functions for phonons and photons emitted from a vibronic molecule in a thermal bath result in bunching and antibunching (a purely quantum effect), respectively. Signatures relating to phonon exchange with the environment are revealed in photon-photon correlations. We demonstrate that cross-correlation functions have a strong dependence on the order of detection giving insight into how phonon dynamics influences the emission of light. This work offers new opportunities to investigate quantum effects in condensed-phase molecular systems.

Astrocytes derived from ASD individuals alter behavior and destabilize neuronal activity through aberrant Ca2+ signaling.

The cellular mechanisms of autism spectrum disorder (ASD) are poorly understood. Cumulative evidence suggests that abnormal synapse function underlies many features of this disease. Astrocytes regulate several key neuronal processes, including the formation of synapses and the modulation of synaptic plasticity. Astrocyte abnormalities have also been identified in the postmortem brain tissue of ASD individuals. However, it remains unclear whether astrocyte pathology plays a mechanistic role in ASD, as opposed to a compensatory response. To address this, we combined stem cell culturing with transplantation techniques to determine disease-specific properties inherent to ASD astrocytes. We demonstrate that ASD astrocytes induce repetitive behavior as well as impair memory and long-term potentiation when transplanted into the healthy mouse brain. These in vivo phenotypes were accompanied by reduced neuronal network activity and spine density caused by ASD astrocytes in hippocampal neurons in vitro. Transplanted ASD astrocytes also exhibit exaggerated Ca2+ fluctuations in chimeric brains. Genetic modulation of evoked Ca2+ responses in ASD astrocytes modulates behavior and neuronal activity deficits. Thus, this study determines that astrocytes derived from ASD iPSCs are sufficient to induce repetitive behavior as well as cognitive deficit, suggesting a previously unrecognized primary role for astrocytes in ASD.

Ongoing Challenges With Price Transparency in Hospital Charges for Hand Procedures.

In 2020, the Centers for Medicare & Medicaid Services issued a historic rule on price transparency that aimed to better inform Americans about their health care costs by requiring hospitals to publicly provide pricing information on their items and services. In this review article, we describe the current gaps in transparency that persist after the implementation of the rule, from incomplete pricing files to noncompliance despite the issuance of monetary penalties by Centers for Medicare & Medicaid Services. Price transparency is vital for hand and upper extremity procedures, given their cost variation and patient desire for more financial discussions with their physicians regarding these procedures. Further improvements and interventions by various stakeholders are necessary to improve the current state of hospital price transparency and cost information for these patients and for anyone who seeks to make informed health care decisions. Policymakers should enforce stronger financial interventions and penalties and promote the use of bundled payments to facilitate better compliance by hospitals through a more expanded and accessible display of health care service costs. To help increase health care financial literacy among consumers, hand surgeons and hospital staff should engage in more dialog regarding health care prices and financial considerations with their patients.

[Mechanism of piRNA in bisphenol A-promoted invasion and migration of prostate cancer cells].

Objective: To investigate the regulatory mechanisms of piwi-interacting RNA (piRNA) in bisphenol A (BPA)-induced prostate cancer cell invasion and migration. Methods: The Cancer Genome Atlas (TCGA) data was used to analyze and screen for piRNAs with significantly increased expression in prostate cancer tissues. PC-3 cells were treated with different concentrations of BPA for 12, 24, and 48 h, respectively, and the 20% inhibitory concentration (IC20) was measured using a CCK-8 assay. The expression levels of piRNAs before and after BPA treatment were determined by reverse transcription-quantitative PCR. Target genes regulated by BPA and associated with prostate cancer were screened in the Comparative Toxicogenomics Database (CTD). Dual-luciferase reporter gene assay was performed to verify the relationship between piRNA and target genes, and the expression change of the piRNA target gene was detected by Western blotting. Cell migration and invasion assays were used to determine the effects of piRNA on the malignant phenotype of prostate cancer cells. Results: After treatment of PC-3 cells with 160 µmol/L BPA, the expression of piR-sno48 was most significantly increased (P<0.05). Transfection of piR-sno48 antagomir resulted in decreased expression of endogenous piR-sno48 and a significant increase in the expression of its target gene GSTP1 (P<0.05). However, the expression of GSTP1 did not change significantly in BPA-treated PC-3 cells after transfection with piR-sno48 antagomir (P>0.05). The dual-luciferase reporter gene confirmed that piR-sno48 inhibited the expression of GSTP1 by forming an inversely complementary sequence with the 3'-UTR of GSTP1. The Transwell assay results showed that treatment with BPA significantly increased the invasion and migration ability of prostate cancer cells (P<0.01), whereas piR-sno48 antagonists significantly inhibited the effects above (P<0.01). Conclusion: BPA promotes the invasion and migration of prostate cancer cells by upregulating the expression of piR-sno48 and suppressing the expression of GSTP1. Interfering with the expression of endogenous piR-sno48 may inhibit the malignant phenotype of prostate cancer cells caused by BPA.

Impact of the COVID-19 pandemic on emergency hospital cancer admissions in a UK region.

BACKGROUND: The pandemic disrupted society and health services through lockdowns and resource reallocation to care for COVID-19 patients. Reductions in numbers of cancer patients having surgery, being diagnosed pathologically or via 2-week wait, and screening programs pauses have been described. The effect on emergency presentation, which represents an acute episode with poor outcomes, has not been investigated. This study explored the pandemic's impact on emergency hospital admissions for cancer patients in a UK region. METHODS: Hospital discharge data for cancer patients in Northern Ireland, which included route to admission, were analysed for the pandemic era in 2020 compared to averages for March to December 2017-2019, focusing on volume and route of emergency admissions by demography and tumour site. FINDINGS: Compared with the pre-pandemic era, the number of cancer emergency admissions fell by 12·3% in 2020. Emergency admissions for cancer were significantly reduced when COVID-19 levels were highest (- 18·5% in April and - 16.8% in October). Females (- 15·8%), urban residents (- 13·2%), and age groups 0 to 49 and 65-74 years old (- 17%) experienced the largest decreases as did those with haematological (- 14·7%), brain and CNS (- 27·9%), and lung cancers(- 14·3%). Significant reductions in referrals from outpatient departments (- 51%) and primary care (- 43%) (p < 0·001) were counterbalanced by admissions from other routes including confirmed or suspected COVID-19 infection (increase 83·6%). INTERPRETATION: Reductions in emergency admissions, and pathologically diagnosed cancers, as reported by the Northern Ireland Cancer Registry (NICR), indicate undiagnosed patients in the community which has implications for future workloads and survival. Data suggest undiagnosed cases may be higher for haematological, brain and CNS, and lung cancers and among females. Efforts should be made to encourage people with symptoms to present for diagnosis or reassurance. FUNDING: The NICR is funded by the Public Health Agency of Northern Ireland. This work was supported by Macmillan Cancer Support and uses data collected by health services as part of their care and support functions.

Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission.

Fitting stochastic transmission models to electronic patient data can offer detailed insights into the transmission of healthcare-associated infections and improve infection control. Pathogen whole-genome sequencing may improve the precision of model inferences, but computational constraints have limited modelling applications predominantly to small datasets and specific outbreaks, whereas large-scale sequencing studies have mostly relied on simple rules for identifying/excluding plausible transmission. We present a novel approach for integrating detailed epidemiological data on patient contact networks in hospitals with large-scale pathogen sequencing data. We apply our approach to study Clostridioides difficile transmission using a dataset of 1223 infections in Oxfordshire, UK, 2007-2011. 262 (21% [95% credibility interval 20-22%]) infections were estimated to have been acquired from another known case. There was heterogeneity by sequence type (ST) in the proportion of cases acquired from another case with the highest rates in ST1 (ribotype-027), ST42 (ribotype-106) and ST3 (ribotype-001). These same STs also had higher rates of transmission mediated via environmental contamination/spores persisting after patient discharge/recovery; for ST1 these persisted longer than for most other STs except ST3 and ST42. We also identified variation in transmission between hospitals, medical specialties and over time; by 2011 nearly all transmission from known cases had ceased in our hospitals. Our findings support previous work suggesting only a minority of C. difficile infections are acquired from known cases but highlight a greater role for environmental contamination than previously thought. Our approach is applicable to other healthcare-associated infections. Our findings have important implications for effective control of C. difficile.

Contribution of warm habitat to cold-water fisheries.

A central tenet of landscape ecology is that mobile species depend on complementary habitats, which are insufficient in isolation, but combine to support animals through the full annual cycle. However, incorporating the dynamic needs of mobile species into conservation strategies remains a challenge, particularly in the context of climate adaptation planning. For cold-water fishes, it is widely assumed that maximum temperatures are limiting and that summer data alone can predict refugia and population persistence. We tested these assumptions in populations of redband rainbow trout (Oncorhynchus mykiss newberrii) in an arid basin, where the dominance of hot, hyperproductive water in summer emulates threats of climate change predicted for cold-water fish in other basins. We used telemetry to reveal seasonal patterns of movement and habitat use. Then, we compared contributions of hot and cool water to growth with empirical indicators of diet and condition (gut contents, weight-length ratios, electric phase angle, and stable isotope signatures) and a bioenergetics model. During summer, trout occurred only in cool tributaries or springs (<20 °C) and avoided Upper Klamath Lake (>25 °C). During spring and fall, ≥65% of trout migrated to the lake (5-50 km) to forage. Spring and fall growth (mean [SD] 0.58% per day [0.80%] and 0.34 per day [0.55%], respectively) compensated for a net loss of energy in cool summer refuges (-0.56% per day [0.55%]). In winter, ≥90% of trout returned to tributaries (25-150 km) to spawn. Thus, although perennially cool tributaries supported thermal refuge and spawning, foraging opportunities in the seasonally hot lake ultimately fueled these behaviors. Current approaches to climate adaptation would prioritize the tributaries for conservation but would devalue critical foraging habitat because the lake is unsuitable and unoccupied during summer. Our results empirically demonstrate that warm water can fuel cold-water fisheries and challenge the common practice of identifying refugia based only on summer conditions.

RESUMEN: Un principio central de la ecología de paisaje es que las especies ambulantes dependen de hábitats complementarios, los cuales son insuficientes en aislamiento, pero al combinarse mantienen a los animales durante el ciclo anual completo. Sin embargo, la incorporación de las necesidades dinámicas de las especies ambulantes dentro de las estrategias de conservación todavía es un reto, particularmente en el contexto de la planeación de la adaptación climática. Para los peces de agua fría, generalmente se asume que las temperaturas máximas son limitantes y que los datos estivales son suficientes para predecir refugios y la persistencia poblacional. Pusimos a prueba estas suposiciones en poblaciones de trucha arcoíris (Oncorhynchus mykiss newberrii) de una cuenca árida, en donde el dominio de aguas cálidas e hiperproductivas durante el verano emula las amenazas del cambio climático pronosticadas para los peces de agua fría en otras cuencas. Usamos telemetría para descubrir los patrones estacionales de movimiento y uso de hábitat. Después, comparamos las contribuciones que tienen las aguas cálidas y frías al crecimiento con indicadores empíricos de dieta y condición (contenidos intestinales, proporciones peso-longitud, ángulo de fase eléctrica y huellas de isotopos estables) y un modelo bioenergético. Durante el verano, las truchas sólo estuvieron presentes en manantiales o afluentes fríos (<20°C) y evitaron el Lago Klamath Superior (>25°C). Durante la primavera y el otoño, ≥65% de las truchas migraron al lago (5-50 km) para procurar alimento. El crecimiento durante la primavera y el otoño (media [SD] 0.58% día-1 [0.80%] y 0.34 día-1 [0.55%], respectivamente) compensaron la pérdida neta de energía en los refugios fríos durante el verano (-0.56% día-1 [0.55%]). En el invierno, ≥90% de las truchas regresaron a los afluentes (25-150 km) para desovar. Entonces, mientras que los afluentes perennemente fríos fomentaron los refugios termales y el desove, fueron las oportunidades de alimentación en el lago cálido estacional las que finalmente alentaron estos comportamientos. Las estrategias actuales de adaptación climática pondrían como prioridad de conservación a los afluentes, pero devaluarían el hábitat crítico de alimentación porque el lago está desocupado y no es apto durante el verano. Nuestros resultados demuestran empíricamente que las aguas cálidas pueden promover las pesquerías de aguas frías y desafiar la práctica común de identificar refugios basándose solamente en las condiciones estivales.

Estimation of the impact of hospital-onset SARS-CoV-2 infections on length of stay in English hospitals using causal inference.

BACKGROUND: From March 2020 through August 2021, 97,762 hospital-onset SARS-CoV-2 infections were detected in English hospitals. Resulting excess length of stay (LoS) created a potentially substantial health and economic burden for patients and the NHS, but we are currently unaware of any published studies estimating this excess. METHODS: We implemented appropriate causal inference methods to determine the extent to which observed additional hospital stay is attributable to the infection rather than the characteristics of the patients. Hospital admissions records were linked to SARS-CoV-2 test data to establish the study population (7.5 million) of all non-COVID-19 admissions to English hospitals from 1st March 2020 to 31st August 2021 with a stay of at least two days. The excess LoS due to hospital-onset SARS-CoV-2 infection was estimated as the difference between the mean LoS observed and in the counterfactual where infections do not occur. We used inverse probability weighted Kaplan-Meier curves to estimate the mean survival time if all hospital-onset SARS-CoV-2 infections were to be prevented, the weights being based on the daily probability of acquiring an infection. The analysis was carried out for four time periods, reflecting phases of the pandemic differing with respect to overall case numbers, testing policies, vaccine rollout and prevalence of variants. RESULTS: The observed mean LoS of hospital-onset cases was higher than for non-COVID-19 hospital patients by 16, 20, 13 and 19 days over the four phases, respectively. However, when the causal inference approach was used to appropriately adjust for time to infection and confounding, the estimated mean excess LoS caused by hospital-onset SARS-CoV-2 was: 2.0 [95% confidence interval 1.8-2.2] days (Mar-Jun 2020), 1.4 [1.2-1.6] days (Sep-Dec 2020); 0.9 [0.7-1.1] days (Jan-Apr 2021); 1.5 [1.1-1.9] days (May-Aug 2021). CONCLUSIONS: Hospital-onset SARS-CoV-2 is associated with a small but notable excess LoS, equivalent to 130,000 bed days. The comparatively high LoS observed for hospital-onset COVID-19 patients is mostly explained by the timing of their infections relative to admission. Failing to account for confounding and time to infection leads to overestimates of additional length of stay and therefore overestimates costs of infections, leading to inaccurate evaluations of control strategies.

The effect of hand hygiene frequency on reducing acute respiratory infections in the community: a meta-analysis.

Hand hygiene is a simple, low-cost intervention that may lead to substantial population-level effects in suppressing acute respiratory infection epidemics. However, quantification of the efficacy of hand hygiene on respiratory infection in the community is lacking. We searched PubMed for randomised controlled trials on the effect of hand hygiene for reducing acute respiratory infections in the community published before 11 March 2021. We performed a meta-regression analysis using a Bayesian mixed-effects model. A total of 105 publications were identified, out of which six studies reported hand hygiene frequencies. Four studies were performed in household settings and two were in schools. The average number of handwashing events per day ranged from one to eight in the control arms, and four to 17 in the intervention arms. We estimated that a single hand hygiene event is associated with a 3% (80% credible interval (-1% to 7%)) decrease in the daily probability of an acute respiratory infection. Three of these six studies were potentially at high risk of bias because the primary outcome depended on self-reporting of upper respiratory tract symptoms. Well-designed trials with an emphasis on monitoring hand hygiene adherence are needed to confirm these findings.