Complete genome sequences of five Ackermannviridae that infect Enterobacteriaceae hosts

This announcement contains the whole genome sequences of five Ackermannviridae that infect members of the Enterobacteriaceae family of bacteria. Four of the five phages were isolated using Salmonella enterica serovar Typhimurium as a bacterial host: AR2819, Sajous1, SilasIsHot, and FrontPhageNews. ChubbyThor was isolated using Shigella boydii.

Insight into the relationship between forced vital capacity and transfer of the lungs for carbon monoxide in patients with idiopathic pulmonary fibrosis

BACKGROUND

Forced vital capacity (FVC) is routinely used to quantify the severity and identify the progression of idiopathic pulmonary fibrosis (IPF). Although less commonly used, lung transfer of carbon monoxide (TLCO) correlates better with the severity of IPF than does FVC.

METHODS

Aiming at studying how FVC behaves in relation to TLCO, we analysed cross-sectional data from 430 IPF patients, of which 221 had at least 2 assessments (performed 2.4 ± 1.9 years apart) available for longitudinal analyses. Thresholds for identifying "abnormal" FVC and TLCO values were the statistically-defined lower limits of normal (LLN). For patients with longitudinal data, mean annual absolute declines of FVC and TLCO were calculated.

RESULTS

The correlation between FVC and TLCO (%predicted) was weak (R2=0.21). FVC was "abnormal" (i.e.,

CONCLUSION

In IPF, a "normal" FVC should be viewed with caution as it is most often associated with an "abnormal" TLCO, a parameter that is strongly correlated with the morphological extent of the disease. Only 1/3 of the patients with a FVC-based progression criterion also had a TLCO progression criterion. In contrast, 2/3 of patients with a TLCO progression criterion also had a FVC progression criterion.

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Key Words

• Forced vital capacity
• Idiopathic pulmonary fibrosis
• Pulmonary function tests
• Transfer of the lungs for carbon monoxide

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MESH Headings

• Humans
• Carbon Monoxide
• Cross-Sectional Studies
• Lung
• Vital Capacity
• Idiopathic Pulmonary Fibrosis/diagnosis

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Cardiometabolic risk management: insights from a European Society of Cardiology Cardiovascular Round Table

Metabolic comorbidities are common in patients with cardiorenal disease; they can cause atherosclerotic cardiovascular disease (ASCVD), speed progression, and adversely affect prognosis. Common comorbidities are Type 2 diabetes mellitus (T2DM), obesity/overweight, chronic kidney disease (CKD), and chronic liver disease. The cardiovascular system, kidneys, and liver are linked to many of the same risk factors (e.g. dyslipidaemia, hypertension, tobacco use, diabetes, and central/truncal obesity), and shared metabolic and functional abnormalities lead to damage throughout these organs via overlapping pathophysiological pathways. The COVID-19 pandemic has further complicated the management of cardiometabolic diseases. Obesity, T2DM, CKD, and liver disease are associated with increased risk of poor outcomes of COVID-19 infection, and conversely, COVID-19 can lead to worsening of pre-existing ASCVD. The high rates of these comorbidities highlight the need to improve recognition and treatment of ASCVD in patients with obesity, insulin resistance or T2DM, chronic liver diseases, and CKD and equally, to improve recognition and treatment of these diseases in patients with ASCVD. Strategies to prevent and manage cardiometabolic diseases include lifestyle modification, pharmacotherapy, and surgery. There is a need for more programmes at the societal level to encourage a healthy diet and physical activity. Many pharmacotherapies offer mechanism-based approaches that can target multiple pathophysiological pathways across diseases. These include sodium-glucose cotransporter-2 inhibitors, glucagon-like peptide-1 receptor agonists, selective mineralocorticoid receptor antagonists, and combined glucose-dependent insulinotropic peptide/glucagon-like peptide-1 receptor agonist. Non-surgical and surgical weight loss strategies can improve cardiometabolic disorders in individuals living with obesity. New biomarkers under investigation may help in the early identification of individuals at risk and reveal new treatment targets.

TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization

Introduction

The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize various body cavities, leading to life-threatening bloodstream infections. However, the identification and characterization of fungal isolates in laboratories remain a significant diagnostic challenge in medicine and public health. Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens.

Methods

TheiaEuk was designed using containerized components and written in the workflow description language (WDL) to facilitate deployment on the cloud-based open bioinformatics platform Terra. This species-agnostic workflow enables the analysis of fungal genomes without requiring coding, thereby reducing the entry barrier for laboratory scientists. To demonstrate the usefulness of this pipeline, an ongoing outbreak of C. auris in southern Nevada was investigated. We performed whole-genome sequence analysis of 752 new C. auris isolates from this outbreak. Furthermore, TheiaEuk was utilized to observe the accumulation of mutations in the FKS1 gene over the course of the outbreak, highlighting the utility of TheiaEuk as a monitor of emerging public health threats when combined with whole-genome sequencing surveillance of fungal pathogens.

Results

A primary result of this work is a curated fungal database containing 5,667 unique genomes representing 245 species. TheiaEuk also incorporates taxon-specific submodules for specific species, including clade-typing for Candida auris (C. auris). In addition, for several fungal species, it performs dynamic reference genome selection and variant calling, reporting mutations found in genes currently associated with antifungal resistance (FKS1, ERG11, FUR1). Using genome assemblies from the ATCC Mycology collection, the taxonomic identification module used by TheiaEuk correctly assigned genomes to the species level in 126/135 (93.3%) instances and to the genus level in 131/135 (97%) of instances, and provided zero false calls. Application of TheiaEuk to actual specimens obtained in the course of work at a local public health laboratory resulted in 13/15 (86.7%) correct calls at the species level, with 2/15 called at the genus level. It made zero incorrect calls. TheiaEuk accurately assessed clade type of Candida auris in 297/302 (98.3%) of instances.

Discussion

TheiaEuk demonstrated effectiveness in identifying fungal species from whole genome sequence. It further showed accuracy in both clade-typing of C. auris and in the identification of mutations known to associate with drug resistance in that organism.

The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks of Candida auris in southern Nevada

A Candida auris outbreak has been ongoing in Southern Nevada since August 2021. In this manuscript we describe the sequencing of over 200 C. auris isolates from patients at several facilities. Genetically distinct subgroups of C. auris were detected from Clade I (3 distinct lineages) and III (1 lineage). Open-source bioinformatic tools were developed and implemented to aid in the epidemiological investigation. The work herein compares three methods for C. auris whole genome analysis: Nullarbor, MycoSNP and a new pipeline TheiaEuk. We also describe a novel analysis method focused on elucidating phylogenetic linkages between isolates within an ongoing outbreak. Moreover, this study places the ongoing outbreaks in a global context utilizing existing sequences provided worldwide. Lastly, we describe how the generated results were communicated to the epidemiologists and infection control to generate public health interventions.

GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking): A methodology to rapidly leverage whole genome sequencing of bacterial isolates for clinical identification

Whole genome sequencing (WGS) of clinical bacterial isolates has the potential to transform the fields of diagnostics and public health. To realize this potential, bioinformatic software that reports identification results needs to be developed that meets the quality standards of a diagnostic test. We developed GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) using k-mer based strategies for identification of bacteria based on WGS reads. GAMBIT incorporates this algorithm with a highly curated searchable database of 48,224 genomes. Herein, we describe validation of the scoring methodology, parameter robustness, establishment of confidence thresholds and the curation of the reference database. We assessed GAMBIT by way of validation studies when it was deployed as a laboratory-developed test in two public health laboratories. This method greatly reduces or eliminates false identifications which are often detrimental in a clinical setting.

Business Versus Ethics? Thoughts on the Future of Business Ethics

To commemorate 40 years since the founding of the Journal of Business Ethics, the editors in chief of the journal have invited the editors to provide commentaries on the future of business ethics. This essay comprises a selection of commentaries aimed at creating dialogue around the theme Business versus Ethics? (inspired by the title of the commentary by Jeffrey Harrison). The authors of these commentaries seek to transcend the age-old separation fallacy (Freeman in Bus Ethics Q 4(4):409-421, 1994) that juxtaposes business and ethics/society, posing a forced choice or trade off. Providing a contemporary take on the classical question "if it's legal is it ethical?", David Hess explores the role of the law in promoting or hindering stakeholder-oriented purpose and governance structure. Jeffrey Harrison encourages scholars to move beyond the presupposition that businesses are either strategic or ethical and explore important questions at the intersection of strategy and ethics. The proposition that business models might be inherently ethical or inherently unethical in their design is developed by Sheila Killian, who examines business systems, their morality, and who they serve. However, the conundrum that entrepreneurs are either lauded for their self-belief and risk-taking, or loathed for their self-belief and risk-taking, is discussed by M. Tina Dacin and Julia Roloff using the metaphor of taboos and totems. These commentaries seek to explore positions that advocate multiplicity and tensions in which business ethics is not either/or but both.

Healthcare-associated infection impact with bioaerosol treatment and COVID-19 mitigation measures

BACKGROUND

The real-world impact of breathing zone air purification and coronavirus disease 2019 (COVID-19) mitigation measures on healthcare-associated infections is not well documented. Engineering solutions to treat airborne transmission of disease may yield results in controlled test chambers or single rooms, but have not been reported on hospital-wide applications, and the impact of COVID-19 mitigation measures on healthcare-associated infection rates is unknown.

AIM

To determine the impact of hospital-wide bioaerosol treatment and COVID-19 mitigation measures on clinical outcomes.

METHODS

The impact of the step-wise addition of air disinfection technology and COVID-19 mitigation measures to standard multi-modal infection control on particle counts, viral and bacterial bioburden, and healthcare-associated infection rates was investigated in a 124-bed hospital (>100,000 patient-days over 30 months).

FINDINGS AND CONCLUSION

The addition of air disinfection technology and COVID-19 mitigation measures reduced airborne ultrafine particles, altered hospital bioburden, and reduced healthcare-associated infections from 11.9 to 6.6 (per 1000 patient-days) and from 6.6 to 1.0 (per 1000 patient-days), respectively (P<0.0001, R2=0.86). No single technology, tool or procedure will eliminate healthcare-associated infections, but the addition of a ubiquitous facility-wide engineering solution at limited expense and with no alteration to patient, visitor or staff traffic or workflow patterns reduced infections by 45%. A similar impact was documented with the addition of comprehensive, restrictive, and labour- and material-intensive COVID-19 mitigation measures. To the authors' knowledge, this is the first direct comparison between traditional infection control, an engineering solution and COVID-19 mitigation measures.

A machine learning approach to predict extreme inactivity in COPD patients using non-activity-related clinical data

Facilitating the identification of extreme inactivity (EI) has the potential to improve morbidity and mortality in COPD patients. Apart from patients with obvious EI, the identification of a such behavior during a real-life consultation is unreliable. We therefore describe a machine learning algorithm to screen for EI, as actimetry measurements are difficult to implement. Complete datasets for 1409 COPD patients were obtained from COLIBRI-COPD, a database of clinicopathological data submitted by French pulmonologists. Patient- and pulmonologist-reported estimates of PA quantity (daily walking time) and intensity (domestic, recreational, or fitness-directed) were first used to assign patients to one of four PA groups (extremely inactive [EI], overtly active [OA], intermediate [INT], inconclusive [INC]). The algorithm was developed by (i) using data from 80% of patients in the EI and OA groups to identify ‘phenotype signatures’ of non-PA-related clinical variables most closely associated with EI or OA; (ii) testing its predictive validity using data from the remaining 20% of EI and OA patients; and (iii) applying the algorithm to identify EI patients in the INT and INC groups. The algorithm’s overall error for predicting EI status among EI and OA patients was 13.7%, with an area under the receiver operating characteristic curve of 0.84 (95% confidence intervals: 0.75–0.92). Of the 577 patients in the INT/INC groups, 306 (53%) were reclassified as EI by the algorithm. Patient- and physician- reported estimation may underestimate EI in a large proportion of COPD patients. This algorithm may assist physicians in identifying patients in urgent need of interventions to promote PA.

Embryonic protein NODAL regulates the breast tumor microenvironment by reprogramming cancer-derived secretomes

The tumor microenvironment (TME) is an important mediator of breast cancer progression. Cancer-associated fibroblasts constitute a major component of the TME and may originate from tissue-associated fibroblasts or infiltrating mesenchymal stromal cells (MSCs). The mechanisms by which cancer cells activate fibroblasts and recruit MSCs to the TME are largely unknown, but likely include deposition of a pro-tumorigenic secretome. The secreted embryonic protein NODAL is clinically associated with breast cancer stage and promotes tumor growth, metastasis, and vascularization. Herein, we show that NODAL expression correlates with the presence of activated fibroblasts in human triple-negative breast cancers and that it directly induces Cancer-associated fibroblasts phenotypes. We further show that NODAL reprograms cancer cell secretomes by simultaneously altering levels of chemokines (e.g., CXCL1), cytokines (e.g., IL-6) and growth factors (e.g., PDGFRA), leading to alterations in MSC chemotaxis. We therefore demonstrate a hitherto unappreciated mechanism underlying the dynamic regulation of the TME.

Abstract PO028: Embryonic protein NODAL as a potential modulator of the tumour microenvironment: Breast cancer secretome reprogramming and fibroblast activation

The tumour microenvironment (TME), consisting of stromal cell types including fibroblasts, endothelial, immune and mesenchymal stromal cells (MSCs), is an important mediator of breast cancer (BCa) progression. BCa cells regulate the composition of the TME by secreting a myriad of factors; however, mechanisms governing the dynamic reciprocity between BCa and TME components are largely unknown. Cancer-associated fibroblasts (CAFs) are a major stromal component in many BCa and have been shown to be activated by BCa cells. MSCs recruited to the TME are an important source of CAFs in many cancers; therefore, characterizing the factors involved in MSC recruitment could provide additional avenues for therapeutic intervention by disrupting the TME in BCa. NODAL, an embryonic morphogen belonging to the TGF-beta superfamily, is clinically associated with BCa progression, and has been shown to sustain BCa stem cells and to promote tumour growth, metastasis, and vascularization. Herein, we report that NODAL expression positively correlates with the presence of CAFs in the stroma of triple-negative human BCa tissues, as determined by NODAL and a-smooth muscle Actin (SMA) staining. Further, our in vitro studies show that NODAL directly induces primary fibroblast activation and chemotaxis. Proteomic analysis of the conditioned media of NODAL-overexpressing MDA-MB-231 and SUM149 BCa cells by mass spectrometry reveal that NODAL reprograms BCa secretomes by simultaneously altering levels of chemokines (e.g. CXCL1), growth factors (e.g. PDGFRA) and cytokines (e.g. IL-6), and that the NODAL-regulated secretome, but not NODAL directly, impacts the ability of BCa cells to affect MSC chemotaxis. We provide evidence that IL-6 promotes MSC chemotaxis, and further discuss the context-dependent effects of NODAL in BCa cell lines. Collectively, our results suggest that factors present in NODAL-regulated secretomes may induce MSC recruitment to the breast TME, where they may contribute to CAF population, therefore demonstrating a hitherto unappreciated role of NODAL as a dynamic regulator of breast TME components.

Citation Format: Dylan Dieters-Castator, Paola M. Dantonio, Matt Piaseczny, Guihua Zhang, Jiahui Liu, Miljan Kuljanin, Stephen Sherman, Michael Jewer, Katherine Quesnel, Eun-Young Kang, Martin Köbel, Gabrielle M. Siegers, Andrew Leask, David Hess, Gilles Lajoie, Lynne-Marie Postovit. Embryonic protein NODAL as a potential modulator of the tumour microenvironment: Breast cancer secretome reprogramming and fibroblast activation [abstract]. In: Proceedings of the AACR Virtual Special Conference on the Evolving Tumor Microenvironment in Cancer Progression: Mechanisms and Emerging Therapeutic Opportunities; in association with the Tumor Microenvironment (TME) Working Group; 2021 Jan 11-12. Philadelphia (PA): AACR; Cancer Res 2021;81(5 Suppl):Abstract nr PO028.

Self- or caregiver-delivered manual remote ischemic conditioning therapy in acute ischemic stroke is feasible: the Early Remote Ischemic Conditioning in Stroke (ERICS) trial

Background: Infarct growth and recurrent stroke may be responsible for early morbidity and mortality in patients with acute ischemic stroke. Remote ischemic conditioning (RIC) may reduce infarct growth and prevent recurrent stroke; however, the exact dose remains to be investigated. We hypothesized that self- or caregiver-delivered six cycles of RIC intervention in acute ischaemic stroke for the first 12 weeks is feasible and safe compared to the four cycles RIC intervention. Methods: Adult ischemic stroke patients presenting within the first 48 h of symptom onset were screened. Patients with magnetic resonance imaging (MRI) evidence of acute infarct were randomized (1:1) to receive either four or six cycles of RIC therapy sessions two times daily in both arms for 12 weeks. All patients underwent MRI for infarct volume assessment and endothelial-dependent flow-mediated dilation (EDFMD) testing at baseline, 7 days and 12 weeks.   Results: A total of 57 patients with mean±SD age of 59.4±12.4 years and median National Institute of Stroke Scale, 4 (IQR, 3-7) were randomised at a median of 23 h 30 min (IQR, 10 h 20 min to 30 h) after symptom onset to either the four-cycle (n=27) or six-cycle group (n=30). A total of 18 (66%) patients completed ≥50% sessions in 12 weeks in the four-cycles group; 21 (69.7%) patients completed ≥50% sessions in 12 weeks in the six-cycle group (p=0.4). There was no between-group differences in infarct growth, early neurological deterioration, recurrent stroke, and EDFMD at 7 days and 90 days. Conclusion: Both four and six cycles of short-term self- or caregiver-delivered RIC therapy is safe and may be feasible in acute ischaemic stroke patients. Randomised clinical trials are needed to assess efficacy to decrease infarct growth and prevent early neurological deterioration. Registration: Clinical Trial Registry - India: CTRI/2016/11/007495; registered on 25/11/2016.

Nelfinavir and lenalidomide/dexamethasone in patients with lenalidomide-refractory multiple myeloma. A phase I/II Trial (SAKK 39/10)

The antiretroviral agent nelfinavir has antimyeloma activity and can overcome resistance to bortezomib. Our phase I/II trial investigated whether adding nelfinavir to lenalidomide-dexamethasone can overcome lenalidomide resistance in lenalidomide-refractory multiple myeloma (MM). Twenty-nine patients were included (high-risk cytogenetic aberrations 31%; ≥2 prior therapy lines 93%; lenalidomide-bortezomib double-refractory 34%). Twenty-four patients (83%) had prior bortezomib and 10 (34%) were lenalidomide-bortezomib double-refractory. They received four cycles of nelfinavir 2500 mg/day with standard-dose lenalidomide (25 mg days 1-21) and dexamethasone (40/20 mg days 1, 8, 15, 22). Minor response or better was achieved in 16 patients (55%; 95% CI 36-74%), including 40% of those who were lenalidomide-bortezomib double-refractory, and partial response or better in nine patients (31%; 95% CI 15-51%). Median progression-free survival was 3.4 (95% CI 2.0-4.9) months and median overall survival 21.6 (13.0-50.1) months. Lenalidomide-related pneumonitis, pneumonia, and neutropenic fever occurred, but there were no unexpected adverse events. Peripheral blood mononuclear cells showed a 45% (95% CI 40-51%) reduction in total proteasome activity from baseline and significant induction of unfolded protein response and autophagy. Thus, nelfinavir-lenalidomide-dexamethasone is an active oral combination in lenalidomide-refractory MM.

Are there specific clinical characteristics associated with physician's treatment choices in COPD?

Background

The number of pharmacological agents and guidelines available for COPD has increased markedly but guidelines remain poorly followed. Understanding underlying clinical reasoning is challenging and could be informed by clinical characteristics associated with treatment prescriptions.

Methods

To determine whether COPD treatment choices by respiratory physicians correspond to specific patients’ features, this study was performed in 1171 patients who had complete treatment and clinical characterisation data. Multiple statistical models were applied to explain five treatment categories: A: no COPD treatment or short-acting bronchodilator(s) only; B: one long-acting bronchodilator (beta2 agonist, LABA or anticholinergic agent, LAMA); C: LABA+LAMA; D: a LABA or LAMA + inhaled corticosteroid (ICS); E: triple therapy (LABA+LAMA+ICS).

Results

Mean FEV1 was 60% predicted. Triple therapy was prescribed to 32.9% (treatment category E) of patients and 29.8% received a combination of two treatments (treatment categories C or D); ICS-containing regimen were present for 44% of patients altogether. Single or dual bronchodilation were less frequently used (treatment categories B and C: 19% each). While lung function was associated with all treatment decisions, exacerbation history, scores of clinical impact and gender were associated with the prescription of > 1 maintenance treatment. Statistical models could predict treatment decisions with a < 35% error rate.

Conclusion

In COPD, contrary to what has been previously reported in some studies, treatment choices by respiratory physicians appear rather rational since they can be largely explained by the patients’ characteristics proposed to guide them in most recommendations.

Electronic supplementary material

The online version of this article (10.1186/s12931-019-1156-1) contains supplementary material, which is available to authorized users.

Trends over time in COPD treatment choices by respiratory physicians: An analysis from the COLIBRI-COPD French cohort

INTRODUCTION

Over the last decade, new evidence and many guidelines have been published on COPD pharmacological treatments; prescriptions are often not in accordance with guidelines.

MATERIALS AND METHODS

Trends in physician treatment choices from February 2012 to November 2018 (Feb.2012/Nov.2018) were analyzed using data from COPD patients (spirometry-confirmed diagnosis) included in the COLIBRI-COPD cohort. Inhaled drug treatments (short- or long-acting β2-agonist [SABA or LABA], short- or long-acting anticholinergic [SAMA or LAMA], or corticosteroid [ICS]) were classified into 5 treatment categories: "No initial maintenance treatment (IMT)" (untreated, or only SAMA or SABA); "1 long-acting bronchodilator (LABD)" (LABA or LAMA); "2 LABDs" (LABA + LAMA); "1 LABD + ICS" (LABA or LAMA + ICS); "2 LABDs + ICS" (LABA + LAMA + ICS). For the purpose of the study, 4 periods were defined to achieve balanced samples (T1-T4).

RESULTS

Data from 4537 patients were collected. Over time, 3 major changes were observed: (1) an increase in treatment category "No IMT", mostly for GOLD 1 or GOLD A categories (GOLD A: from 19.1% at T1 to 41.2% at T4); (2) an increase in treatment category "2 LABDs" for GOLD 2 to 4 and GOLD A to D categories (GOLD B: from 15.4% to 29.7%); (3) a decrease in ICS use ("1 LABD + ICS" or "2 LABDs + ICS"), mostly for GOLD 1 to 3 and GOLD A categories (GOLD A, 2 LABDs + ICS: from 35.3% to 11.1%).

CONCLUSION

Changes over time in therapeutic profiles suggest that new evidence from scientific publications and recommendations may have had a rapid impact on clinical practice.

The crystal structures of benzylammonium phenylacetate and its hydrate

The crystal packing of benzyl­ammonium phenyl­acetate (1) and its hydrate (2) is governed by hydrogen bonds formed between the ammonium and acetate groups and the water mol­ecule of crystallization (in 2 only). The benzyl moieties for hydro­phobic layers with the aromatic rings adopting edge-to-face arrangements.

The title compounds benzyl­ammonium phenyl­acetate, C₇H₁₀N⁺·C₈H₇O₂⁻ (1), and its monohydrate, C₇H₁₀N⁺·C₈H₇O₂⁻·H₂O (2), can be obtained by evaporating methano­lic solutions containing equimolar amounts of benzyl­amine and phenyl­acetic acid in the absence and presence of water, respectively. N—H⋯O hydrogen bonds in the crystal structure of 1 lead to the formation of hydro­philic channels running along the b-axis direction. The hydrogen-bonding system is best described by fused R³₄(10) ring patterns, often observed in ammonium carboxyl­ate salts. In 2, the presence of the crystal water leads to the formation of a two-dimensional hydrogen-bonding network. The benzyl moieties in 1 and 2 form hydro­phobic layers in the crystal structures with the aromatic rings adopting edge-to-face arrangements.