Multiplex detection of the big five carbapenemase genes using solid-phase recombinase polymerase amplification.

Five carbapenemase enzymes, coined the 'big five', have been identified as the biggest threat to worldwide antibiotic resistance based on their broad substrate affinity and global prevalence. Here we show the development of a molecular detection method for the gene sequences from the five carbapenemases utilising the isothermal amplification method of recombinase polymerase amplification (RPA). We demonstrate the successful detection of each of the big five carbapenemase genes with femtomolar detection limits using a spatially separated multiplex amplification strategy. The approach uses tailed oligonucleotides for hybridisation, reducing the complexity and cost of the assay compared to classical RPA detection strategies. The reporter probe, horseradish peroxidase, generates the measureable output on a benchtop microplate reader, but more notably, our study leverages the power of a portable Raman spectrometer, enabling up to a 19-fold enhancement in the limit of detection. Significantly, the development approach employed a solid-phase RPA format, wherein the forward primers targeting each of the five carbapenemase genes are immobilised to a streptavidin-coated microplate. The adoption of this solid-phase methodology is pivotal for achieving a successful developmental pathway when employing this streamlined approach. The assay takes 2 hours until result, including a 40 minutes RPA amplification step at 37 °C. This is the first example of using solid-phase RPA for the detection of the big five and represents a milestone towards the developments of an automated point-of-care diagnostic for the big five using RPA.

Soft Contact Mechanics with Gradient-Stiffness Surfaces.

The stiffness in the top surface of many biological entities like cornea or articular cartilage, as well as chemically cross-linked synthetic hydrogels, can be significantly lower or more compliant than the bulk. When such a heterogeneous surface comes into contact, the contacting load is distributed differently from typical contact models. The mechanical response under indentation loading of a surface with a gradient of stiffness is a complex, integrated response that necessarily includes the heterogeneity. In this work, we identify empirical contact models between a rigid indenter and gradient elastic surfaces by numerically simulating quasi-static indentation. Three key case studies revealed the specific ways in which (I) continuous gradients, (II) laminate-layer gradients, and (III) alternating gradients generate new contact mechanics at the shallow-depth limit. Validation of the simulation-generated models was done by micro- and nanoindentation experiments on polyacrylamide samples synthesized to have a softer gradient surface layer. The field of stress and stretch in the subsurface as visualized from the simulations also reveals that the gradient layers become confined, which pushes the stretch fields closer to the surface and radially outward. Thus, contact areas are larger than expected, and average contact pressures are lower than predicted by the Hertz model. The overall findings of this work are new contact models and the mechanisms by which they change. These models allow a more accurate interpretation of the plethora of indentation data on surface gradient soft matter (biological and synthetic) as well as a better prediction of the force response to gradient soft surfaces. This work provides examples of how gradient hydrogel surfaces control the subsurface stress distribution and loading response.

Recent advances in antibiotic resistance diagnosis using SERS: focus on the "Big 5" challenges.

Antibiotic resistant bacteria constitute a global health threat. It is essential for healthcare professionals to prescribe the correct dose of an effective antibiotic to mitigate the bacterial infection in a timely manner to improve the therapeutic outcomes to the patient and prevent the dissemination of antibiotic resistance. To achieve this, there is a need to implement a rapid and ultra-sensitive clinical diagnosis to identify resistant bacterial strains and monitor the effect of antibiotics. In this review, we highlight the use of surface enhanced Raman scattering (SERS) as a powerful diagnostic technique for bacterial detection and evaluation. Initially, this is viewed through a lens covering why SERS can surpass other traditional techniques for bacterial diagnosis. This is followed by different SERS substrates design, detection strategies that have been used for various bacterial biomarkers, how SERS can be combined with other diagnostic platforms to improve its performance towards the bacterial detection and the application of SERS for antibiotic resistance diagnosis. Finally, the recent progress in SERS detection methods in the last decade for the "Big 5" antibiotic resistant challenges as demonstrators of public health major threats is reviewed, namely: Methicillin-resistant Staphylococcus aureus (MRSA), Carbapenem-resistant Enterobacteriaceae (CRE)/Extended-spectrum beta-lactamases (ESBLs), Mycobacterium tuberculosis (TB), Vancomycin-resistant Enterococcus (VRE) and Neisseria Gonorrhoea (NG). This review provides a comprehensive view of the current state of the art with regard to using SERS for assessing antibiotic resistance with a future outlook on where the field go head in the coming years.

Patient Perceptions on Barriers and Facilitators to Accessing Low-acuity Surgery During COVID-19 Pandemic.

BACKGROUND: The onset of the COVID-19 pandemic led to the postponement of low-acuity surgical procedures in an effort to conserve resources and ensure patient safety. This study aimed to characterize patient-reported concerns about undergoing surgical procedures during the pandemic. METHODS: We administered a cross-sectional survey to patients who had their general and plastic surgical procedures postponed at the onset of the pandemic, asking about barriers to accessing surgical care. Questions addressed dependent care, transportation, employment and insurance status, as well as perceptions of and concerns about COVID-19. Mixed methods and inductive thematic analyses were conducted. RESULTS: One hundred thirty-five patients were interviewed. We identified the following patient concerns: contracting COVID-19 in the hospital (46%), being alone during hospitalization (40%), facing financial stressors (29%), organizing transportation (28%), experiencing changes to health insurance coverage (25%), and arranging care for dependents (18%). Nonwhite participants were 5 and 2.5 times more likely to have concerns about childcare and transportation, respectively. Perceptions of decreased hospital safety and the consequences of possible COVID-19 infection led to delay in rescheduling. Education about safety measures and communication about scheduling partially mitigated concerns about COVID-19. However, uncertainty about timeline for rescheduling and resolution of the pandemic contributed to ongoing concerns. CONCLUSIONS: Providing effective surgical care during this unprecedented time requires both awareness of societal shifts impacting surgical patients and system-level change to address new barriers to care. Eliciting patients' perspectives, adapting processes to address potential barriers, and effectively educating patients about institutional measures to minimize in-hospital transmission of COVID-19 should be integrated into surgical care.

Rapid ultra-sensitive diagnosis of clostridium difficile infection using a SERS-based lateral flow assay.

Clostridium difficile (C. diff) infection is one of the most contagious diseases associated with high morbidity and mortality rates in hospitalised patients. Accurate diagnosis can slow its spread by determining the most effective treatment. Herein, we report a novel testing platform as a proof-of-concept for the selective, sensitive, rapid and cost-effective diagnosis of C. diff infection (CDI) based on a duplex measurement. This was achieved by detecting two specific biomarkers, surface layer protein A (SlpA) and toxin B (ToxB), using a surface enhanced Raman scattering-based lateral flow assay (SERS-based LFA). The simultaneous duplex detection of SlpA with ToxB has not been described for the clinical diagnosis of CDI previously. The SlpA biomarker "AKDGSTKEDQLVDALA" was first reported by our group in 2018 as a species-specific identification tool. The second biomarker, ToxB, is the essential virulence biomarker of C. diff pathogenic strains and is required to confirm true infection pathogenicity. The proposed SERS-based LFA platform enabled rapid duplex detection of SlpA and ToxB on separate test lines using a duplex LF test strip within 20 minutes. The use of a handheld Raman spectrometer to scan test lines allowed for the highly sensitive quantitative detection of both biomarkers with a lowest observable concentration of 0.01 pg µL-1. The use of a handheld device in this SERS-based LFA instead of benchtop machine paves the way for rapid, selective, sensitive and cheap clinical evaluation of CDI at the point of care (POC) with minimal sample backlog.

Helix N-Cap Residues Drive the Acid Unfolding That Is Essential in the Action of the Toxin Colicin A.

Numerous bacterial toxins and other virulence factors use low pH as a trigger to convert from water-soluble to membrane-inserted states. In the case of colicins, the pore-forming domain of colicin A (ColA-P) has been shown both to undergo a clear acidic unfolding transition and to require acidic lipids in the cytoplasmic membrane, whereas its close homologue colicin N shows neither behavior. Compared to that of ColN-P, the ColA-P primary structure reveals the replacement of several uncharged residues with aspartyl residues, which upon replacement with alanine induce an unfolded state at neutral pH. Here we investigate ColA-P's structural requirement for these critical aspartyl residues that are largely situated at the N-termini of α helices. As previously shown in model peptides, the charged carboxylate side chain can act as a stabilizing helix N-Cap group by interacting with free amide hydrogen bond donors. Because this could explain ColA-P destabilization when the aspartyl residues are protonated or replaced with alanyl residues, we test the hypothesis by inserting asparagine, glutamine, and glutamate residues at these sites. We combine urea (fluorescence and circular dichroism) and thermal (circular dichroism and differential scanning calorimetry) denaturation experiments with 1H-15N heteronuclear single-quantum coherence nuclear magnetic resonance spectroscopy of ColA-P at different pH values to provide a comprehensive description of the unfolding process and confirm the N-Cap hypothesis. Furthermore, we reveal that, in urea, the single domain ColA-P unfolds in two steps; low pH destabilizes the first step and stabilizes the second.

The Two-State Prehensile Tail of the Antibacterial Toxin Colicin N.

Intrinsically disordered regions within proteins are critical elements in many biomolecular interactions and signaling pathways. Antibacterial toxins of the colicin family, which could provide new antibiotic functions against resistant bacteria, contain disordered N-terminal translocation domains (T-domains) that are essential for receptor binding and the penetration of the Escherichia coli outer membrane. Here we investigate the conformational behavior of the T-domain of colicin N (ColN-T) to understand why such domains are widespread in toxins that target Gram-negative bacteria. Like some other intrinsically disordered proteins in the solution state of the protein, ColN-T shows dual recognition, initially interacting with other domains of the same colicin N molecule and later, during cell killing, binding to two different receptors, OmpF and TolA, in the target bacterium. ColN-T is invisible in the high-resolution x-ray model and yet accounts for 90 of the toxin's 387 amino acid residues. To reveal its solution structure that underlies such a dynamic and complex system, we carried out mutagenic, biochemical, hydrodynamic and structural studies using analytical ultracentrifugation, NMR, and small-angle x-ray scattering on full-length ColN and its fragments. The structure was accurately modeled from small-angle x-ray scattering data by treating ColN as a flexible system, namely by the ensemble optimization method, which enables a distribution of conformations to be included in the final model. The results reveal, to our knowledge, for the first time the dynamic structure of a colicin T-domain. ColN-T is in dynamic equilibrium between a compact form, showing specific self-recognition and resistance to proteolysis, and an extended form, which most likely allows for effective receptor binding.

The antibacterial toxin colicin N binds to the inner core of lipopolysaccharide and close to its translocator protein.

Colicins are a diverse family of large antibacterial protein toxins, secreted by and active against Escherichia coli and must cross their target cell's outer membrane barrier to kill. To achieve this, most colicins require an abundant porin (e.g. OmpF) plus a low-copy-number, high-affinity, outer membrane protein receptor (e.g. BtuB). Recently, genetic screens have suggested that colicin N (ColN), which has no high-affinity receptor, targets highly abundant lipopolysaccharide (LPS) instead. Here we reveal the details of this interaction and demonstrate that the ColN receptor-binding domain (ColN-R) binds to a specific region of LPS close to the membrane surface. Data from in vitro studies using calorimetry and both liquid- and solid-state NMR reveal the interactions behind the in vivo requirement for a defined oligosaccharide region of LPS. Delipidated LPS (LPS(Δ) (LIPID) ) shows weaker binding; and thus full affinity requires the lipid component. The site of LPS binding means that ColN will preferably bind at the interface and thus position itself close to the surface of its translocon component, OmpF. ColN is, currently, unique among colicins in requiring LPS and, combined with previous data, this implies that the ColN translocon is distinct from those of other known colicins.

The unstructured domain of colicin N kills Escherichia coli.

Bacteria often produce toxins which kill competing bacteria. Colicins, produced by and toxic to Escherichia coli bacteria are three-domain proteins so efficient that one molecule can kill a cell. The C-terminal domain carries the lethal activity and the central domain is required for surface receptor binding. The N-terminal domain, required for translocation across the outer membrane, is always intrinsically unstructured. It has always been assumed therefore that the C-terminal cytotoxic domain is required for the bactericidal activity. Here we report the unexpected finding that in isolation, the 90-residue unstructured N-terminal domain of colicin N is cytotoxic. Furthermore it causes ion leakage from cells but, unlike known antimicrobial peptides (AMPs) with this property, shows no membrane binding behaviour. Finally, its activity remains strictly dependent upon the same receptor proteins (OmpF and TolA) used by full-length colicin N. This mechanism of rapid membrane disruption, via receptor mediated binding of a soluble peptide, may reveal a new target for the development of highly specific antibacterials.

Low resolution structure and dynamics of a colicin-receptor complex determined by neutron scattering.

Proteins that translocate across cell membranes need to overcome a significant hydrophobic barrier. This is usually accomplished via specialized protein complexes, which provide a polar transmembrane pore. Exceptions to this include bacterial toxins, which insert into and cross the lipid bilayer itself. We are studying the mechanism by which large antibacterial proteins enter Escherichia coli via specific outer membrane proteins. Here we describe the use of neutron scattering to investigate the interaction of colicin N with its outer membrane receptor protein OmpF. The positions of lipids, colicin N, and OmpF were separately resolved within complex structures by the use of selective deuteration. Neutron reflectivity showed, in real time, that OmpF mediates the insertion of colicin N into lipid monolayers. This data were complemented by Brewster Angle Microscopy images, which showed a lateral association of OmpF in the presence of colicin N. Small angle neutron scattering experiments then defined the three-dimensional structure of the colicin N-OmpF complex. This revealed that colicin N unfolds and binds to the OmpF-lipid interface. The implications of this unfolding step for colicin translocation across membranes are discussed.

Disparities in advance care planning rates persist among emergency general surgery patients: Current state and recommendations for improvement.

BACKGROUND: Unanticipated changes in health status and worsening of chronic conditions often prompt the need to consider emergency general surgery (EGS). Although discussions about goals of care may promote goal-concordant care and reduce patient and caregiver depression and anxiety, these conversations, as well as standardized documentation, remain infrequent for EGS patients. METHODS: We conducted a retrospective cohort study using electronic health record data from patients admitted to an EGS service at a tertiary academic center to determine the prevalence of clinically meaningful advance care planning (ACP) documentation (conversations and legal ACP forms) during the EGS hospitalization. Multivariable regression was performed to identify patient, clinician, and procedural factors associated with the lack of ACP. RESULTS: Among 681 patients admitted to the EGS service in 2019, only 20.1% had ACP documentation in the electronic health record at any time point during their hospitalization (of those, 75.5% completed before and 24.5% completed during admission). Two thirds (65.8%) of the total cohort had surgery during their admission, but none of them had a documented ACP conversation with the surgical team preoperatively. Patients with ACP documentation tended to have Medicare insurance (adjusted odds ratio, 5.06; 95% confidence interval, 2.09-12.23; p < 0.001) and had greater burden of comorbid conditions (adjusted odds ratio, 4.19; 95% confidence interval, 2.55-6.88; p < 0.001). CONCLUSION: Adults experiencing a significant, often abrupt change in health status leading to an EGS admission are infrequently engaged in ACP conducted by the surgical team. This is a critical missed opportunity to promote patient-centered care and to communicate patients' care preferences to the surgical and other inpatient medical teams. LEVEL OF EVIDENCE: Therapeutic/Care Management; Level IV.

Composition controls soft hydrogel surface layer dimensions and contact mechanics.

Hydrogels are soft hydrated polymer networks that are widely used in research and industry due to their favorable properties and similarity to biological tissues. However, it has long been difficult to create a hydrogel emulating the heterogeneous structure of special tissues, such as cartilage. One potential avenue to develop a structural variation in a hydrogel is the "mold effect," which has only recently been discovered to be caused by absorbed oxygen within the mold surface interfering with the polymerization. This induces a dilute gradient-density surface layer with altered properties. However, the precise structure of the gradient-surface layer and its contact response have not yet been characterized. Such knowledge would prove useful for designs of composite hydrogels with altered surface characteristics. To fully characterize the hydrogel gradient-surface layer, we created five hydrogel compositions of varying monomer and cross-linker content to encompass variations in the layer. Then, we used particle exclusion microscopy during indentation and creep experiments to probe the contact response of the gradient layer of each composition. These experiments showed that the dilute structure of the gradient layer follows evolving contact behavior allowing poroelastic squeeze-out at miniscule pressures. Stiffer compositions had thinner gradient layers. This knowledge can potentially be used to create hydrogels with a stiff load-bearing bulk with altered surface characteristics tailored for specific tribological applications.

Non-operative management of pneumoperitoneum following cardiopulmonary resuscitation.

Spontaneous pneumoperitoneum in a patient with a tracheostomy tube following cardiopulmonary resuscitation is exceedingly rare, with little experimental nor observational data to guide evidence-based management. We present the case of a 75-year-old woman with a tracheostomy tube who developed pneumoperitoneum following CPR. The patient experienced pulseless electrical activity arrest requiring nine rounds of chest compressions to return to spontaneous circulation. Computerized tomography demonstrated pneumothoraces, subcutaneous emphysema and extensive intraperitoneal, extraperitoneal and retroperitoneal free air without evidence of visceral perforation. The patient's abdomen was distended without tenderness, guarding or rebound. She had a white blood cell count mildly elevated from her baseline levels. The management plan of serial abdominal exams without operative intervention was chosen given the absence of clinical and laboratory signs of peritonitis. This case highlights the importance of developing a standardized management algorithm for patients with pneumoperitoneum in the setting of tracheostomy tubes without evidence of perforation.

Lessons From Learners: Adapting Medical Student Education During and Post COVID-19.

In response to the COVID-19 pandemic, many medical schools suspended clinical clerkships and implemented newly adapted curricula to facilitate continued educational progress. While the implementation of these new curricula has been described, an understanding of the impact on student learning outcomes is lacking. In 2020, the authors followed Kern's 6-step approach to curricular development to create and evaluate a novel COVID-19 curriculum for medical students at the University of California San Francisco School of Medicine and evaluate its learning outcomes. The primary goal of the curriculum was to provide third- and fourth-year medical students an opportunity for workplace learning in the absence of clinical clerkships, specifically for students to develop clerkship-level milestones in the competency domains of practice-based learning and improvement, professionalism, and systems-based practice. The curriculum was designed to match students with faculty-mentored projects occurring primarily in virtual formats. A total of 126 students enrolled in the curriculum and completed a survey about their learning outcomes (100% response rate). Of 35 possible clerkship-level milestones, there were 12 milestones for which over half of students reported development in competency domains including practice-based learning and improvement, professionalism, and interpersonal and communication skills. Thematic analysis of students' qualitative survey responses demonstrated 2 central motivations for participating in the curriculum: identity as physicians-in-training and patient engagement. Six central learning areas were developed during the curriculum: interprofessional teamwork, community resources, technology in medicine, skill-building, quality improvement, and specialty-specific learning. This analysis demonstrates that students can develop competencies and achieve rich workplace learning through project-based experiential learning, even in virtual clinical workplaces. Furthermore, knowledge of community resources, technology in medicine, and quality improvement was developed through the curriculum more readily than in traditional clerkships. These could be considered as integral learning objectives in future curricular design.

Interfacial interactions of pore-forming colicins.

Colicins are water soluble toxins secreted by E. coli cells to kill other E. coli and related species. To do this they need to cross the outer membrane, periplasm and inner membrane. Pore forming colicins, as their name suggests form a voltage dependent pore in the inner membrane. This chapter deals with the interfaces, both lipid and protein, that the colicins experience as they make the short but complex journey that brings them to the point of pore formation. The succession of molecular interactions with lipid and protein receptors causes a series of conformational changes which allow these large > 40 kDa proteins to outwit the normally tight defensive shield of the target cell. This is done by combining general physico-chemical interfacial interactions, such as the use of amphipathic helical peptides, with precisely targeted protein-protein interactions involving both rigid and natively disordered protein domains.