Is it COVID-19? The value of medicolegal autopsies during the first year of the COVID-19 pandemic.

OBJECTIVES: We describe the experience of a busy metropolitan medical examiner's office in the United States and share our navigation of the COVID-19 autopsy decision-making process. We describe key gross and microscopic findings that, with appropriate laboratory testing, should direct a pathologist towards a COVID-19-related cause of death. MATERIAL AND METHODS: We performed a retrospective review of 258 suspected and/or confirmed COVID-19 associated deaths that occurred between March 5, 2020, and March 4, 2021. RESULTS: A total of 62 cases due to fatal COVID-19 were identified; autopsy findings included diffuse alveolar damage, acute bronchopneumonia and lobar pneumonia, and pulmonary thromboemboli. Nine additional decedents had a nasopharyngeal swab positive for SARS-CoV-2 and a cause of death unrelated to COVID-19. Forty-seven cases with COVID-19-like symptoms showed no laboratory or histopathologic evidence of SARS-CoV-2 infection; the most common causes of death in this group were hypertensive or atherosclerotic cardiovascular disease, complications of chronic alcoholism, and pulmonary thromboemboli unrelated to infection. CONCLUSIONS: The clinical findings associated with COVID-19 are not specific; a broad differential diagnosis should be embraced when decedents present with cough or shortness of breath. An autopsy may be indicated to identify a cause of death unrelated to COVID-19.

Harnessing motivation for sustainable practice change: From passive receivers to active co-creators.

OBJECTIVES: The challenges of implementing clinical practice changes are well recognised. Prevailing approaches to tackling them have largely relied on increasing control and standardisation, but with limited impact. We examine research from the behavioural sciences in an attempt to (a) build a clearer understanding of why the implementation of change in clinical settings has proved so elusive and (b) provide practical guidance on how organisations can create a climate that can nurture sustained behavioural change in their workforce. METHOD: We undertook a review of the behavioural science literature to gain a better understanding of the circumstances under which staff might willingly pursue goals that are externally generated. Three studies, derived from the mental health literature, are outlined to illustrate how the manner in which change is introduced can have a significant effect on its uptake and sustainability. RESULTS: Research suggests that human behaviour is not as unpredictable as it might at first appear; rather, there are some deeply rooted, psychological processes at play. Self-Determination Theory, a theory of human motivation with an extensive body of research supporting its effectiveness, suggests that the manner in which change is introduced and implemented is critical. CONCLUSION: While improvement methodologies and the use of implementation strategies are necessary, experience would suggest that by themselves they are not sufficient. Overcoming the challenges of implementing change will require a significant shift in our thinking about organisational leadership and the way that change is introduced. Some practical ways leaders can foster staff buy-in for organisational change are proposed.

Probing Pharmaceutical Mixtures during Milling: The Potency of Low-Frequency Raman Spectroscopy in Identifying Disorder.

This study uses a multimodal analytical approach to evaluate the rates of (co)amorphization of milled drug and excipient and the effectiveness of different analytical methods in detecting these changes. Indomethacin and tryptophan were the model substances, and the analytical methods included low-frequency Raman spectroscopy (785 nm excitation and capable of measuring both low- (10 to 250 cm-1) and midfrequency (450 to 1800 cm-1) regimes, and a 830 nm system (5 to 250 cm-1)), conventional (200-3000 cm-1) Raman spectroscopy, Fourier transform infrared spectroscopy (FTIR), and X-ray powder diffraction (XRPD). The kinetics of amorphization were found to be faster for the mixture, and indeed, for indomethacin, only partial amorphization occurred (after 360 min of milling). Each technique was capable of identifying the transformations, but some, such as low-frequency Raman spectroscopy and XRPD, provided less ambiguous signatures than the midvibrational frequency techniques (conventional Raman and FTIR). The low-frequency Raman spectra showed intense phonon mode bands for the crystalline and cocrystalline samples that could be used as a sensitive probe of order. Multivariate analysis has been used to further interpret the spectral changes. Overall, this study demonstrates the potential of low-frequency Raman spectroscopy, which has several practical advantages over XRPD, for probing (dis-)order during pharmaceutical processing, showcasing its potential for future development, and implementation as an in-line process monitoring method.

You can lead a horse to water what Self-Determination Theory can contribute to our understanding of clinical policy implementation.

There has been increasing reliance on policy directives as instruments for shaping clinical practice in health care, despite it being widely recognized that there is a significant translation gap between clinical policy and its implementation. Self-Determination Theory, a widely researched and empirically validated theory of human needs' fulfilment and motivation, offers a potentially valuable theoretical framework for understanding not only why the current policy environment has not led to the anticipated improvement in the quality and safety of clinical care but, importantly, also provides guidance about how organizations can create an environment that can nurture behavioural change in the workforce. We describe an alternative approach to clinical policy-making underpinned by Self-Determination Theory, which we believe has broad application for the science of clinical implementation theory.

From providing a service to being of service: advances in person-centred care in mental health.

PURPOSE OF REVIEW: This review explores the concept of person-centred care, giving particular attention to its application in mental health and its relationship to recovery. It then outlines a framework for understanding the variety of approaches that have been used to operationalize person-centred care, focusing particularly on shared decision-making and self-directed care, two practices that have significant implications for mental health internationally. RECENT FINDINGS: Despite growing recognition of person-centred care as an essential component of recovery-orientated practice, the levels of uptake of shared decision-making and self-directed care in mental health remain low. The most significant barrier appears to be the challenge presented to service providers by one of the key principles of person-centred care, namely empowerment. SUMMARY: Shared decision-making and self-directed support, two practices based upon the principles of person-centred care, have the potential for being effective tools for recovery. Full engagement of clinicians is crucial for their successful uptake into practice. More research is needed to address both outcomes and implementation.

High-throughput sequencing of DNA G-quadruplex structures in the human genome.

G-quadruplexes (G4s) are nucleic acid secondary structures that form within guanine-rich DNA or RNA sequences. G4 formation can affect chromatin architecture and gene regulation and has been associated with genomic instability, genetic diseases and cancer progression. Here we present a high-resolution sequencing-based method to detect G4s in the human genome. We identified 716,310 distinct G4 structures, 451,646 of which were not predicted by computational methods. These included previously uncharacterized noncanonical long loop and bulged structures. We observed a high G4 density in functional regions, such as 5' untranslated regions and splicing sites, as well as in genes previously not predicted to contain these structures (such as BRCA2). G4 formation was significantly associated with oncogenes, tumor suppressors and somatic copy number alterations related to cancer development. The G4s identified in this study may therefore represent promising targets for cancer intervention.

Raman imaging of drug delivery systems.

This review article includes an introduction to the principals of Raman spectroscopy, an outline of the experimental systems used for Raman imaging and the associated important considerations and limitations of this method. Common spectral analysis methods are briefly described and examples of interesting published studies which utilised Raman imaging of pharmaceutical and biomedical devices are discussed, along with summary tables of the literature at this point in time.

Evaluating the introduction of joint crisis plans into routine clinical practice in four community mental health services.

OBJECTIVE: Our aim was to evaluate the implementation of joint crisis planning into routine clinical practice in community mental health services in Western Australia. METHOD: Four community mental health services, two metropolitan and two country based, were invited to participate in a 1-year pilot program to field test a crisis planning tool and the implementation process with a view to then rolling it out across Western Australia. Training and extensive support was offered to staff at the four sites. RESULTS: Consumers experienced the process as both empowering and therapeutic. Despite acknowledgement of the value of interagency collaboration in the planning process, almost all plans were completed by consumers with their case managers. The most conspicuous finding was the marked difference in the number of completed plans at each site. CONCLUSIONS: This study supports previous research findings that joint crisis planning enhances the therapeutic relationship and empowers consumers. Organisational readiness was a major factor in the differential uptake of crisis plans between sites. Our study highlights the critical importance of addressing the context and culture of each individual service in which a new intervention is being introduced as part of the implementation process.

To see, or not to see, that is the question: can public disclosure really improve transparency between medicine and the pharmaceutical industry?

OBJECTIVE: To critically review the potential effect of the public reporting of pharmaceutical company payments to healthcare professionals on the relationship between medicine and industry. METHOD: This review is based on an examination of the 'Transparency Model' put out recently for consultation by Medicines Australia. RESULTS: Public reporting in itself will neither sharpen the boundaries between medicine and the pharmaceutical industry nor restore public confidence. CONCLUSIONS: Focusing on payments for clinical research and on the larger payments to healthcare professionals would lead to a better understanding of the interplay between science and marketing.

Rapid single-colony whole-genome sequencing of bacterial pathogens.

OBJECTIVES: As a result of the introduction of rapid benchtop sequencers, the time required to subculture a bacterial pathogen to extract sufficient DNA for library preparation can now exceed the time to sequence said DNA. We have eliminated this rate-limiting step by developing a protocol to generate DNA libraries for whole-genome sequencing directly from single bacterial colonies grown on primary culture plates. METHODS: We developed our protocol using single colonies of 17 bacterial pathogens responsible for severe human infection that were grown using standard diagnostic media and incubation conditions. We then applied this method to four clinical scenarios that currently require time-consuming reference laboratory tests: full identification and genotyping of salmonellae; identification of blaNDM-1, a highly transmissible carbapenemase resistance gene, in Klebsiella pneumoniae; detection of genes encoding staphylococcal toxins associated with specific disease syndromes; and monitoring of vaccine targets to detect vaccine escape in Neisseria meningitidis. RESULTS: We validated our single-colony whole-genome sequencing protocol for all 40 combinations of pathogen and selective, non-selective or indicator media tested in this study. Moreover, we demonstrated the clinical value of this method compared with current reference laboratory tests. CONCLUSIONS: This advance will facilitate the implementation of whole-genome sequencing into diagnostic and public health microbiology.

Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology.

IMPORTANCE: The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens. OBJECTIVE: To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens. DESIGN, SETTING, AND PARTICIPANTS: A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information. MAIN OUTCOMES AND MEASURES: Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data. RESULTS: We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these. CONCLUSIONS AND RELEVANCE: The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance.

A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4.

IMPORTANCE: Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain. OBJECTIVE: To explore the potential of metagenomics, which is the direct sequencing of DNA extracted from microbiologically complex samples, as an open-ended clinical discovery platform capable of identifying and characterizing bacterial strains from an outbreak without laboratory culture. DESIGN, SETTING, AND PATIENTS: In a retrospective investigation, 45 samples were selected from fecal specimens obtained from patients with diarrhea during the 2011 outbreak of Shiga-toxigenic Escherichia coli (STEC) O104:H4 in Germany. Samples were subjected to high-throughput sequencing (August-September 2012), followed by a 3-phase analysis (November 2012-February 2013). In phase 1, a de novo assembly approach was developed to obtain a draft genome of the outbreak strain. In phase 2, the depth of coverage of the outbreak strain genome was determined in each sample. In phase 3, sequences from each sample were compared with sequences from known bacteria to identify pathogens other than the outbreak strain. MAIN OUTCOMES AND MEASURES: The recovery of genome sequence data for the purposes of identification and characterization of the outbreak strain and other pathogens from fecal samples. RESULTS: During phase 1, a draft genome of the STEC outbreak strain was obtained. During phase 2, the outbreak strain genome was recovered from 10 samples at greater than 10-fold coverage and from 26 samples at greater than 1-fold coverage. Sequences from the Shiga-toxin genes were detected in 27 of 40 STEC-positive samples (67%). In phase 3, sequences from Clostridium difficile, Campylobacter jejuni, Campylobacter concisus, and Salmonella enterica were recovered. CONCLUSIONS AND RELEVANCE: These results suggest the potential of metagenomics as a culture-independent approach for the identification of bacterial pathogens during an outbreak of diarrheal disease. Challenges include improving diagnostic sensitivity, speeding up and simplifying workflows, and reducing costs.

A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak.

OBJECTIVES: Epidemiological investigations of Legionnaires' disease outbreaks rely on the rapid identification and typing of clinical and environmental Legionella isolates in order to identify and control the source of infection. Rapid bacterial whole-genome sequencing (WGS) is an emerging technology that has the potential to rapidly discriminate outbreak from non-outbreak isolates in a clinically relevant time frame. METHODS: We performed a pilot study to determine the feasibility of using bacterial WGS to differentiate outbreak from non-outbreak isolates collected during an outbreak of Legionnaires' disease. Seven Legionella isolates (three clinical and four environmental) were obtained from the reference laboratory and sequenced using the Illumina MiSeq platform at Addenbrooke's Hospital, Cambridge. Bioinformatic analysis was performed blinded to the epidemiological data at the Wellcome Trust Sanger Institute. RESULTS: We were able to distinguish outbreak from non-outbreak isolates using bacterial WGS, and to confirm the probable environmental source. Our analysis also highlighted constraints, which were the small number of Legionella pneumophila isolates available for sequencing, and the limited number of published genomes for comparison. CONCLUSIONS: We have demonstrated the feasibility of using rapid WGS to investigate an outbreak of Legionnaires' disease. Future work includes building larger genomic databases of L pneumophila from both clinical and environmental sources, developing automated data interpretation software, and conducting a cost-benefit analysis of WGS versus current typing methods.

Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak.

Two Southeast Asian students attending the same school in the United Kingdom presented with pulmonary tuberculosis. An epidemiological investigation failed to link the two cases, and drug resistance profiles of the Mycobacterium tuberculosis isolates were discrepant. Whole-genome sequencing of the isolates found them to be genetically identical, suggesting a missed transmission event.

Characterization of a verocytotoxin-producing enteroaggregative Escherichia coli serogroup O111:H21 strain associated with a household outbreak in Northern Ireland.

A strain of Escherichia coli O111:H21 recently isolated in the United Kingdom harbored the phage-encoded vtx2c gene and the aggregative adherence plasmid. Although exhibiting the same pathogenic profile as the E. coli O104:H4 strain linked to the outbreak in Germany, there were important differences in strain characteristics and in the epidemiological setting.

Highly sensitive profiling of CD44+/CD24- breast cancer stem cells by combining global mRNA amplification and next generation sequencing: evidence for a hyperactive PI3K pathway.

We performed next generation sequencing- and microarray-based gene expression profiling of CD44(+)/CD24(-)/CD45(-) breast CSCs (cancer stem cells) isolated from primary ERα-positive breast cancer. By combining semi-automated dissociation of human tumor tissue, magnetic cell sorting and cDNA amplification less than 500 CSCs were required for transcriptome analyses. Besides overexpressing genes involved in maintenance of stemness, the CSCs showed higher levels of genes that drive the PI3K pathway, including EGFR, HB-EGF, PDGFRA/B, PDGF, MET, PIK3CA, PIK3R1 and PIK3R2. This suggests that, in CSCs of ERα-positive breast cancer, the PI3K pathway which is involved in endocrine resistance is hyperactive.

Genomic variation among contemporary Pseudomonas aeruginosa isolates from chronically infected cystic fibrosis patients.

The airways of individuals with cystic fibrosis (CF) often become chronically infected with unique strains of the opportunistic pathogen Pseudomonas aeruginosa. Several lines of evidence suggest that the infecting P. aeruginosa lineage diversifies in the CF lung niche, yet so far this contemporary diversity has not been investigated at a genomic level. In this work, we sequenced the genomes of pairs of randomly selected contemporary isolates sampled from the expectorated sputum of three chronically infected adult CF patients. Each patient was infected by a distinct strain of P. aeruginosa. Single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were identified in the DNA common to the paired isolates from different patients. The paired isolates from one patient differed due to just 1 SNP and 8 indels. The paired isolates from a second patient differed due to 54 SNPs and 38 indels. The pair of isolates from the third patient both contained a mutS mutation, which conferred a hypermutator phenotype; these isolates cumulatively differed due to 344 SNPs and 93 indels. In two of the pairs of isolates, a different accessory genome composition, specifically integrated prophage, was identified in one but not the other isolate of each pair. We conclude that contemporary isolates from a single sputum sample can differ at the SNP, indel, and accessory genome levels and that the cross-sectional genomic variation among coeval pairs of P. aeruginosa CF isolates can be comparable to the variation previously reported to differentiate between paired longitudinally sampled isolates.