Demographic fluctuations in bloodstream Staphylococcus aureus lineages configure the mobile gene pool and antimicrobial resistance.

Staphylococcus aureus in the bloodstream causes high morbidity and mortality, exacerbated by the spread of multidrug-resistant and methicillin-resistant S. aureus (MRSA). We aimed to characterize the circulating lineages of S. aureus from bloodstream infections and the contribution of individual lineages to resistance over time. Here, we generated 852 high-quality short-read draft genome sequences of S. aureus isolates from patient blood cultures in a single hospital from 2010 to 2022. A total of 80 previously recognized sequence types (ST) and five major clonal complexes are present in the population. Two frequently detected lineages, ST5 and ST8 exhibited fluctuating demographic structures throughout their histories. The rise and fall in their population growth coincided with the acquisition of antimicrobial resistance, mobile genetic elements, and superantigen genes, thus shaping the accessory genome structure across the entire population. These results reflect undetected selective events and changing ecology of multidrug-resistant S. aureus in the bloodstream.

Prognostic clinical decision support for pneumonia in the emergency department: A randomized trial.

BACKGROUND: Hospitalization rates for childhood pneumonia vary widely. Risk-based clinical decision support (CDS) interventions may reduce unwarranted variation. METHODS: We conducted a pragmatic randomized trial in two US pediatric emergency departments (EDs) comparing electronic health record (EHR)-integrated prognostic CDS versus usual care for promoting appropriate ED disposition in children (<18 years) with pneumonia. Encounters were randomized 1:1 to usual care versus custom CDS featuring a validated pneumonia severity score predicting risk for severe in-hospital outcomes. Clinicians retained full decision-making authority. The primary outcome was inappropriate ED disposition, defined as early transition to lower- or higher-level care. Safety and implementation outcomes were also evaluated. RESULTS: The study enrolled 536 encounters (269 usual care and 267 CDS). Baseline characteristics were similar across arms. Inappropriate disposition occurred in 3% of usual care encounters and 2% of CDS encounters (adjusted odds ratio: 0.99, 95% confidence interval: [0.32, 2.95]) Length of stay was also similar and adverse safety outcomes were uncommon in both arms. The tool's custom user interface and content were viewed as strengths by surveyed clinicians (>70% satisfied). Implementation barriers include intrinsic (e.g., reaching the right person at the right time) and extrinsic factors (i.e., global pandemic). CONCLUSIONS: EHR-based prognostic CDS did not improve ED disposition decisions for children with pneumonia. Although the intervention's content was favorably received, low subject accrual and workflow integration problems likely limited effectiveness. Clinical Trials Registration: NCT06033079.

Association of ambulance diversion policy on EMS transport and ambulance patient offload times: A comparison of three strategies.

Objectives: Despite limited supporting data, hospitals continue to apply ambulance diversion (AD). Thus, we examined the impact of three different diversion policies on diversion hours, transport time (TT; leaving scene to arrival at the hospital), and ambulance patient offload time (APOT; arrival at the hospital to patient turnover to hospital staff) for 9-1-1 transports in a 22-hospital county Emergency Medical Services (EMS) system.Methods: This retrospective study evaluated metrics during periods of three AD policies, each 27 days long: hospital-initiated (Period 1), complete suspension (Period 2), and County EMS-initiated (Period 3). We described the median transports and diversion hours, and compared the daily average and daily 90th percentile TT and APOT during the three study periods.Results: Over the study period, there were 50,992 total transports in the county; Period 3 had fewer median transports per day than Period 1 (581 vs 623, p < 0.001), while Period 2 was similar to Period 1 (606 vs 623, p = 0.108). Median average daily diversion hours decreased from 98.1 hours during Period 1 to zero hours during both Periods 2 (p < 0.001) and 3 (p < 0.001). Median daily average TT decreased from 18.3 minutes in Period 1 to 16.9 minutes in both Periods 2 (p < 0.001) and 3 (p < 0.001). Median daily 90th percentile TT showed a similar decrease from 30.2 minutes in Period 1 to 27.5 in Period 2 (p < 0.001), and to 28.1 in Period 3 (p = 0.001). Median average daily APOT was 26.0 minutes during Period 1, similar at 25.2 minutes during Period 2 (p = 826) and decreased to 20.4 minutes during Period 3 (p < 0.001). The median daily 90th percentile APOT was 53.9 minutes during Period 1, similar at 51.7 minutes during Period 2 (p = 0.553) and decreased to 40.3 minutes during Period 3 (p < 0.001).Conclusions: Compared to hospital-initiated AD, enacting no AD or County EMS-initiated AD was associated with less diversion time; TT and APOT showed statistically significant improvement without hospital-initiated AD but were of unclear clinical significance. EMS-initiated AD was difficult to interpret as that period had significantly fewer transports. EMS systems should consider these findings when developing strategies to improve TT, APOT, and system use of diversion.

Evaluating the impact of hot water killing larvae on gene expression using the transformer gene in Cochliomyia macellaria (Diptera: Calliphoridae).

In forensic entomology, determining the age of a larva from a body to estimate time since death is commonly performed through the measurement of a physical trait. Gene expression has been studied as an alternative age estimation approach, but the storage conditions required for these studies are different than those used in forensic entomological casework. Studies analyzing gene expression prioritize the preservation of RNA, which requires fresh tissue and ultra-cold storage. Casework, in contrast, utilizes hot water killing specimens that may not be analyzed for a long period after collection. In the current study, the impact of hot water killing on gene expression was assessed for larval samples of the forensically important blow fly, Cochliomyia macellaria. Successful amplification of the sex-determining gene, transformer, was tested across larvae ranging in size from 3.22 to 16.85 mm in length after storage times of 1-2 weeks, 4-5 weeks, and 8-9 weeks at 4°C in RNAlater. Larvae hot water killed were processed in tandem with larvae stored live to allow for a direct assessment of the impact of boiling on gene expression. As expected, the transformer gene was successfully amplified in all larvae stored live. For the hot water-killed larvae, the success rate was only slightly lower, with 3 out of 75 larvae not generating a sex-specific band pattern. The results show gene expression can be used for hot water-killed samples, though future work across different genes, species, and extending to quantitative gene expression methods is needed.

Generalized Periodic Discharges Associated With Catatonia and Delirium: A Case Series.

OBJECTIVE: Generalized periodic discharges are a repeated and generalized electroencephalography (EEG) pattern that can be seen in the context of altered mental status. This article describes a series of five individuals with generalized periodic discharges who demonstrated signs and symptoms of catatonia, a treatable neuropsychiatric condition. METHODS: Inpatients with a clinical diagnosis of catatonia, determined with the Bush-Francis Catatonia Rating Scale (BFCRS), and EEG recordings with generalized periodic discharges were analyzed in a retrospective case series. RESULTS: Five patients with catatonia and generalized periodic discharges on EEG were evaluated from among 106 patients with catatonia and contemporaneous EEG measurements. Four of these patients showed an improvement in catatonia severity when treated with benzodiazepines, with an average reduction of 6.75 points on the BFCRS. CONCLUSIONS: Among patients with generalized periodic discharges, catatonia should be considered, in the appropriate clinical context. Patients with generalized periodic discharges and catatonia may benefit from treatment with empiric trials of benzodiazepines.

Adherence to Parkinson's disease medication: A case study to illustrate reasons for non-adherence, implications for practice and engaging under-represented participants in research.

Parkinson's disease (PD) is a progressive neurodegenerative disease which primarily presents with the core symptoms of rigidity, postural instability, tremor, and bradykinesia. Non-adherence to prescribed PD treatments can have significant ramifications, such as poor symptom control and greater disease burden. Reasons for poor adherence are multifaceted, particularly when medication regimens are complex and often based on perceptual and practical barriers. Additionally, engaging fully non-adherent patients in research is challenging since they may have dropped out of service provision, yet their contribution is vital to fully understand the rationale for non-adherence. This paper aims to present a case study on the perspectives of one person with PD, a participant in a previously published qualitative study investigating the barriers and facilitators to medication adherence in PD. In this paper, the participant's diagnostic journey is described, and experiences of medical consultations are summarised to explain their reasons for not adhering to any of the standard UK PD treatments prescribed. The participant's preferences for using Vitamin B1 (thiamine) injections to manage the symptoms are reported and the rationale for doing so is discussed. We consider the case through the lens of a behavioural science approach, drawing on health psychology theory, the Theoretical Domains Framework (TDF), to inform the review and the practical challenges faced when analysing the data for this participant. Implications for pharmacy practice, in particular, are also put forward with view to ensuring that patients such as Mr. Wilkinson are provided with the opportunity to discuss treatment choices and self-management of long-term conditions such as PD. We also discuss the importance of reaching under-represented members of the population in medication adherence research, which embraces the principles of equality, diversity, and inclusion in research.

Optimizing Advanced Trauma Life Support (ATLS®) to Maximize Readiness.

INTRODUCTION: The Army utilizes Individual Critical Task Lists (ICTLs) to track and ensure competency and deployment readiness of its medical service members. ICTLs are the various skills and procedures that the Army has deemed foundational for each area of concentration (AOC)/military occupational specialty (MOS). While many ICTLs involve the patient care that military medical providers regularly provide, some procedures are not as commonly performed. This, when coupled with lower patient volume at military treatment facilities (MTF), poses a challenge for maintaining skill competency and deployment readiness. Fort Campbell's Blanchfield Army Community Hospital (BACH) has created a holistic and unique solution to meet many of these standardized requirements and support a ready medical force. By optimizing the Advanced Trauma Life Support (ATLS®) course curriculum to facilitate ICTL completion, BACH has increased its ICTL completion rates, ATLS® course exposure, and streamlined training requirements. The purpose of this article is to describe this best practice and suggest its applicability to other MTFs. MATERIALS AND METHODS: By cross-referencing the ATLS® course curriculum and appendices with ICTLs, BACH has augmented ATLS® course certification with the additional completion of 12 ICTLs. This new approach not only increases ICTL completion, but also increases ATLS® curriculum exposure to medical providers, such as Registered Nurses or Nurse Practitioners, who would not typically take ATLS®. RESULTS: Since starting this new approach in April 2021, 73 military medical personnel have completed the ATLS® course at BACH, with 24 different medical specialties represented. A total of 361 ICTLs have been completed with specific ICTL completion counts ranging from 13 to 48. Each ICTL tested was completed 100% of its annual requirement. CONCLUSION: ATLS® is a mandatory joint interoperability standard for military physicians and it is also an Army ICTL for many AOCs/MOSs. Only counting completion of this course as one ICTL is a missed opportunity for the time spent by Army medical providers and limits the exposure of ATLS® to select AOCs/MOSs. This optimized and novel approach has been successful at BACH, suggesting its applicability at other MTFs that serve as ATLS® testing sites.

Reproducible mass spectrometry data processing and compound annotation in MZmine 3.

Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Depending on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis. MZmine is an open-source software for the processing of raw spectral data generated by different MS platforms. Examples include liquid chromatography-MS, gas chromatography-MS and MS-imaging. These data might typically be associated with various applications including metabolomics and lipidomics. Moreover, the third version of the software, described herein, supports the processing of ion mobility spectrometry (IMS) data. The present protocol provides three distinct procedures to perform feature detection and annotation of untargeted MS data produced by different instrumental setups: liquid chromatography-(IMS-)MS, gas chromatography-MS and (IMS-)MS imaging. For training purposes, example datasets are provided together with configuration batch files (i.e., list of processing steps and parameters) to allow new users to easily replicate the described workflows. Depending on the number of data files and available computing resources, we anticipate this to take between 2 and 24 h for new MZmine users and nonexperts. Within each procedure, we provide a detailed description for all processing parameters together with instructions/recommendations for their optimization. The main generated outputs are represented by aligned feature tables and fragmentation spectra lists that can be used by other third-party tools for further downstream analysis.

Diagnostic features of paediatric catatonia: multisite retrospective cohort study.

BACKGROUND: Catatonia is a neuropsychiatric disorder characterised by psychomotor changes that can affect individuals across the lifespan. Although features of catatonia have been described in adults, the most common clinical symptoms among paediatric patients with catatonia are not well characterised. AIMS: The goal of this study was to characterise the symptoms of catatonia demonstrated by paediatric patients, and to explore demographic and diagnostic factors associated with greater catatonia severity. METHOD: We conducted a multicentre retrospective cohort study, from 1 January 2018 to 6 January 2023, of patients aged 18 and younger with a clinical diagnosis of catatonia and symptom assessment using the Bush Francis Catatonia Rating Scale (BFCRS). RESULTS: A total of 143 patients met inclusion criteria. The median age was 15 (interquartile range: 13-16) years and 66 (46.2%) patients were female. Neurodevelopmental disabilities were present in 55 (38.5%) patients. Patients demonstrated a mean of 6.0 ± 2.1 signs of catatonia on the Bush Francis Catatonia Screening Item, with a mean BFCRS score of 15.0 ± 5.9. Among the 23 items of the BFCRS, six were present in >50% of patients (staring, mutism, immobility/stupor, withdrawal, posturing/catalepsy, rigidity), and four were present in <20% of cases (waxy flexibility, mitgehen, gegenhalten, grasp reflex). In an adjusted model, patients with neurodevelopmental disorders demonstrated greater BFCRS severity than those with other diagnoses. CONCLUSIONS: Catatonia was diagnosed in a range of mental health conditions. Further research is needed to define optimal diagnostic criteria for catatonia in paediatric patients, and clarify the clinical course of the disorder.

A Genome Wide CRISPR Profiling Approach Identifies Mechanisms of Cisplatin Resistance in Head and Neck Squamous Cell Carcinoma.

Background: Head and neck squamous cell carcinoma (HNSCC) is a lethal disease with poor survival rates, especially for cancers arising in the oral cavity or larynx. Cisplatin is a key chemotherapeutic for HNSCC; however poor survival rates may be partially due to cisplatin resistance observed in some HNSCCs. Here, we examined the utility of genome-wide CRISPR knockout profiling for nominating pivotal mechanisms of cisplatin resistance in HNSCC models. Methods: We characterized the cisplatin sensitivity of 18 HNSCC cell lines. Next, we used a genome-wide CRISPR/Cas9 library to identify genes involved in cisplatin resistance. We next performed validation assays in the UM-SCC-49 cell line model. Results: Our data prioritized 207 genes as pivotal for cisplatin resistance in HNSCC, including novel genes VGLL3, CIRHA1, NCOR1, SPANXA1, MAP2K7, ULK1, and CDK16. Gene set enrichment analysis identified several NOTCH family genes comprising the top pathway driving cisplatin resistance, which we then validated using a targeted NOTCH1 knockout model. Interestingly, we noted that HNSCC models with natural NOTCH pathway alterations including single allele mutations and/or frameshift alterations had diverse responses to cisplatin treatment suggesting that complex and multi-faceted mechanisms contribute to cisplatin resistance in HNSCC. Conclusions: Collectively, our study validates a genome-wide CRISPR/Cas9 approach for the discovery of resistance mechanisms in HNSCC, adds to the growing evidence that NOTCH1 status should be evaluated as a biomarker of cisplatin response and provides a framework for future work aimed at overcoming cisplatin resistance.

Assessing the role of biomarker feedback in a 12-week community weight management programme among overweight men: A pilot study.

BACKGROUND: The primary objective of this study was to examine the feasibility of recruitment, retention, and delivery of biomarker feedback among men partaking in Shape Up, a physical activity for health programme. Secondarily, it explored the potential effects of biomarker feedback on participants' adherence and motivation levels. METHODS: In this two-arm non-randomised pilot study, 46 men (mean±SD age 46.0±8.6 years) participating in the 12-week Shape Up programme were assigned to a control group or biomarker feedback group. Biomarker feedback consisted of 3 blood test panels: at baseline, 12 weeks, and 24 weeks (follow-up), each with a doctor's report. Both groups completed questionnaires (Short Active Lives Survey [SALS], Treatment Self-Regulation Questionnaire [TSRQ], and EQ-5D-5L) to gauge levels of motivation and engagement. The mean difference was calculated between baseline and programme end. Recruitment, retention, and attendance rates were determined. RESULTS: Mean recruitment (approach-to-consent), retention, and attendance rates were 96.3%, 92.3%, and 83.7% in the control group, and 85.2%, 86.2%, and 81.5% in the biomarker feedback group, respectively. Of biomarker feedback group participants, 86.4% attended their 12-week blood test and 45.5% attended their follow-up blood test. The mean 12-week differences (95% CI) for the control group and biomarker feedback group were 138.1 (2.7, 273.5) and 467.3 (249.4, 685.2) for active minutes per week, 0.2 (-0.8, 1.2) and 0.4 (0.0, 0.8) for autonomous TSRQ domains, 0.2 (-0.3, 0.8) and 0.8 (0.1, 1.4) for controlled TSRQ domains, and 19 (12.7, 26.5) and 27.2 (19.8, 34.6) for EQ-5D-5L scores, respectively. CONCLUSION: Biomarker feedback was well-received by participants and deemed feasible, with high recruitment and retention rates for the duration of the 12-week programme. Biomarker feedback may affect aspects of motivation but did not appear to influence adherence to the programme. Biomarker data may provide additional evidence of programme efficacy. Important design considerations are provided for definitive larger-scale trials.

TICI: a taxon-independent community index for eDNA-based ecological health assessment.

Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to provide a reliable, robust and low-cost assessment of ecological health that is accessible to environmental managers, decision makers, and the wider community.

Natural language processing to identify lupus nephritis phenotype in electronic health records.

BACKGROUND: Systemic lupus erythematosus (SLE) is a rare autoimmune disorder characterized by an unpredictable course of flares and remission with diverse manifestations. Lupus nephritis, one of the major disease manifestations of SLE for organ damage and mortality, is a key component of lupus classification criteria. Accurately identifying lupus nephritis in electronic health records (EHRs) would therefore benefit large cohort observational studies and clinical trials where characterization of the patient population is critical for recruitment, study design, and analysis. Lupus nephritis can be recognized through procedure codes and structured data, such as laboratory tests. However, other critical information documenting lupus nephritis, such as histologic reports from kidney biopsies and prior medical history narratives, require sophisticated text processing to mine information from pathology reports and clinical notes. In this study, we developed algorithms to identify lupus nephritis with and without natural language processing (NLP) using EHR data from the Northwestern Medicine Enterprise Data Warehouse (NMEDW). METHODS: We developed five algorithms: a rule-based algorithm using only structured data (baseline algorithm) and four algorithms using different NLP models. The first NLP model applied simple regular expression for keywords search combined with structured data. The other three NLP models were based on regularized logistic regression and used different sets of features including positive mention of concept unique identifiers (CUIs), number of appearances of CUIs, and a mixture of three components (i.e. a curated list of CUIs, regular expression concepts, structured data) respectively. The baseline algorithm and the best performing NLP algorithm were externally validated on a dataset from Vanderbilt University Medical Center (VUMC). RESULTS: Our best performing NLP model incorporated features from both structured data, regular expression concepts, and mapped concept unique identifiers (CUIs) and showed improved F measure in both the NMEDW (0.41 vs 0.79) and VUMC (0.52 vs 0.93) datasets compared to the baseline lupus nephritis algorithm. CONCLUSION: Our NLP MetaMap mixed model improved the F-measure greatly compared to the structured data only algorithm in both internal and external validation datasets. The NLP algorithms can serve as powerful tools to accurately identify lupus nephritis phenotype in EHR for clinical research and better targeted therapies.

Use of the spider limb positioner for fibular free flap reconstruction of head and neck bony defects.

BACKGROUND: Osseous and osteocutaneous fibular free flaps are the workhorse of maxillomandibular reconstruction over 30 years after the initial description. Since 2019, we have routinely used the Spider Limb Positioner, adapted from its use in shoulder orthopedic procedures, for fibular free flap harvest. Herein, we describe this novel technique in our cohort. METHODS: We describe our intraoperative setup and endorse the versatility and utility of this technique in comparison to other reported fibular free flap harvest techniques. RESULTS: The Spider Limb Positioner was used 61 times in 60 different patients to harvest osseous or osteocutaneous fibular free flaps. Median (range) tourniquet time for flap harvest was 90 (40-124) minutes. No iatrogenic nerve compression injuries or complications related to lower extremity positioning occurred. CONCLUSION: We describe a novel approach to fibular free flap harvest utilizing the Spider Limb Positioner, which affords optimal ergonomics, visibility, and patient repositioning. There were no nerve injuries or complications related to positioning in our series.

Updated adult ferritin reference intervals based on a large, healthy UK sample, measured on Roche Cobas series analysers.

BACKGROUND: There is a lack of standardization of reference intervals (RIs) for ferritin across laboratories, particularly for postmenopausal women. Depending on the RI used, there can be more than a 4-fold difference in the upper limit of normal between laboratories, resulting in potential misinterpretation. METHODS: This retrospective study used a large dataset of blood test results from 25,425 healthy participants aged 18 to 97 over a 7-year period. Exclusion criteria were used to screen out individuals with conditions known to affect iron metabolism or raise ferritin as part of the acute phase response. Distributions were assessed using density and Q-Q plots, and age-banded cut-offs were determined. The non-parametric method was used to establish RIs for sex and age bands. RESULTS: For females, 4 age bands were established (18-39, 40-49, 50-59 and 60+). For males, 2 bands were identified (18-39 and 40+). Performance against a validation dataset, followed by an expansive validation against an inclusive dataset, demonstrated the robustness of the derived RIs. CONCLUSION: This study addresses the inconsistency in serum ferritin RIs by presenting intervals based on demographic parameters. This approach can potentially enhance the accuracy of interpreting serum ferritin levels, assisting clinicians in identifying patients requiring further evaluation.