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Abstract Spatially explicit simulations of gene flow within complex landscapes could help forecast the responses of populations to global and anthropological changes. Simulating how past climate change shaped intraspecific genetic variation can provide a validation of models in anticipation of their use to predict future changes. We review simulation models that provide inferences on population genetic structure. Existing simulation models generally integrate complex demographic and genetic processes but are less focused on the landscape dynamics. In contrast to previous approaches integrating detailed demographic and genetic processes and only secondarily landscape dynamics, we present a model based on parsimonious biological mechanisms combining habitat suitability and cellular processes, applicable to complex landscapes. The simulation model takes as input (a) the species dispersal capacities as the main biological parameter, (b) the species habitat suitability, and (c) the landscape structure, modulating dispersal. Our model emphasizes the role of landscape features and their temporal dynamics in generating genetic differentiation among populations within species. We illustrate our model on caribou/reindeer populations sampled across the entire species distribution range in the Northern Hemisphere. We show that simulations over the past 21 kyr predict a population genetic structure that matches empirical data. This approach looking at the impact of historical landscape dynamics on intraspecific structure can be used to forecast population structure under climate change scenarios and evaluate how species range shifts might induce erosion of genetic variation within species.

Digital twin technology is a virtual depiction of a physical product and has been utilized in many fields. Digital twin patient model in healthcare is a virtual patient that provides opportunities to test the outcomes of various interventions virtually without subjecting an actual patient to possible harm. This can serve as a decision aid in the complex environment of the intensive care unit (ICU). Our objective is to develop consensus among a multidisciplinary expert panel on statements regarding respiratory pathophysiology contributing to respiratory failure in the medical ICU. We convened a panel of 34 international critical care experts. Our group modeled elements of respiratory failure pathophysiology using directed acyclic graphs (DAGs) and derived expert statements describing associated ICU clinical practices. The experts participated in three rounds of modified Delphi to gauge agreement on 78 final questions (13 statements with 6 substatements for each) using a Likert scale. A modified Delphi process achieved agreement for 62 of the final expert rule statements. Statements with the highest degree of agreement included the physiology, and management of airway obstruction decreasing alveolar ventilation and ventilation-perfusion matching. The lowest agreement statements involved the relationship between shock and hypoxemic respiratory failure due to heightened oxygen consumption and dead space. Our study proves the utility of a modified Delphi method to generate consensus to create expert rule statements for further development of a digital twin-patient model with acute respiratory failure. A substantial majority of expert rule statements used in the digital twin design align with expert knowledge of respiratory failure in critically ill patients.

Background: Shotgun and targeted metagenomic sequencing have been shown in separate studies to be potentially useful for culture-free pathogen identification in blood and/or plasma of patients with infective endocarditis (IE). However, the 2 approaches have not been directly compared. The aim of this study was to compare shotgun metagenomic sequencing with targeted metagenomic sequencing (tMGS) for organism identification in blood or plasma of patients with IE., Methods: Patients with possible or definite IE were prospectively enrolled from October 2020 to July 2021. Shotgun metagenomic sequencing was performed with the Karius test, which uses microbial cell-free DNA (mcfDNA) sequencing to detect, identify, and quantitate DNA-based pathogens in plasma. tMGS was performed using a 16S ribosomal RNA (rRNA) polymerase chain reaction assay targeting the V1 to V3 regions of the 16S rRNA gene. Results were compared using the McNemar test of paired proportions., Results: Samples from 34 patients were investigated. The Karius test was positive in 24/34 (71%), including 3/6 (50%) with blood culture-negative endocarditis (BCNE), which was not significantly different from the positivity rate of tMGS ( P = .41). Results of the Karius test were concordant with tMGS in 75% of cases. The Karius test detected 2 cases of methicillin-resistant Staphylococcus aureus among the 7 S. aureus detections, in accordance with results of phenotypic susceptibility testing. The combination of blood cultures, the Karius test, and tMGS found a potential causative pathogen in 33/34 (97%), including 5/6 with BCNE., Conclusions: The Karius test and tMGS yielded comparable detection rates; however, beyond organism identification, the Karius test generated potentially useful antibiotic resistance data., Competing Interests: Potential conflicts of interest. L.F., C.R.F., and M.W. have no conflicts of interest. R.P. reports grants from ContraFect, TenNor Therapeutics Limited, and BioFire. R.P. is a consultant to Curetis, Specific Technologies, Next Gen Diagnostics, PathoQuest, Selux Diagnostics, 1928 Diagnostics, PhAST, Torus Biosystems, Day Zero Diagnostics, Mammoth Biosciences, and Qvella; monies are paid to Mayo Clinic. Mayo Clinic and Dr. Patel have relationships with Adaptive Phage Therapeutics and Pathogenomix. R.P. is also a consultant to Netflix and CARB-X. In addition, R.P. has a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic, and a patent on an antibiofilm substance issued. R.P. receives honoraria from the NBME, Up-to-Date, and the Infectious Diseases Board Review Course. All other authors report no potential conflicts., (© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Sequencing is increasingly used for infective endocarditis (IE) diagnosis. Here, the performance of 16S rRNA gene PCR/sequencing of heart valves utilized in routine clinical practice was compared with conventional IE diagnostics. Subjects whose heart valves were sent to the clinical microbiology laboratory for 16S rRNA gene PCR/sequencing from August 2020 through February 2022 were studied. A PCR assay targeting V1 to V3 regions of the 16S rRNA gene was performed, followed by Sanger and/or next-generation sequencing (NGS) (using an Illumina MiSeq), or reported as negative, depending on an algorithm that included the PCR cycle threshold value. Fifty-four subjects, including 40 with IE, three with cured IE, and 11 with noninfective valvular disease, were studied. Thirty-one positive results, 11 from NGS and 20 from Sanger sequencing, were generated from analysis of 16S rRNA gene sequence(s). Positivity rates of blood cultures and 16S rRNA gene PCR/sequencing of valves were 55% and 75%, respectively ( P  = 0.06). In those with prior antibiotic exposure, positivity rates of blood cultures and 16S rRNA gene PCR/sequencing of valves were 11% and 76%, respectively ( P < 0.001). Overall, 61% of blood culture-negative IE subjects had positive valve 16S rRNA gene PCR/sequencing results. 16S rRNA gene-based PCR/sequencing of heart valves is a useful diagnostic tool for pathogen identification in patients with blood culture-negative IE undergoing valve surgery in routine clinical practice., Competing Interests: The authors declare no conflict of interest.

Introduction: Digital twins, a form of artificial intelligence, are virtual representations of the physical world. In the past 20 years, digital twins have been utilized to track wind turbines' operations, monitor spacecraft's status, and even create a model of the Earth for climate research. While digital twins hold much promise for the neurocritical care unit, the question remains on how to best establish the rules that govern these models. This model will expand on our group's existing digital twin model for the treatment of sepsis., Methods: The authors of this project collaborated to create a Direct Acyclic Graph (DAG) and an initial series of 20 DELPHI statements, each with six accompanying sub-statements that captured the pathophysiology surrounding the management of acute ischemic strokes in the practice of Neurocritical Care (NCC). Agreement from a panel of 18 experts in the field of NCC was collected through a 7-point Likert scale with consensus defined a-priori by ≥ 80% selection of a 6 ("agree") or 7 ("strongly agree"). The endpoint of the study was defined as the completion of three separate rounds of DELPHI consensus. DELPHI statements that had met consensus would not be included in subsequent rounds of DELPHI consensus. The authors refined DELPHI statements that did not reach consensus with the guidance of de-identified expert comments for subsequent rounds of DELPHI. All DELPHI statements that reached consensus by the end of three rounds of DELPHI consensus would go on to be used to inform the construction of the digital twin model., Results: After the completion of three rounds of DELPHI, 93 (77.5%) statements reached consensus, 11 (9.2%) statements were excluded, and 16 (13.3%) statements did not reach a consensus of the original 120 DELPHI statements., Conclusion: This descriptive study demonstrates the use of the DELPHI process to generate consensus among experts and establish a set of rules for the development of a digital twin model for use in the neurologic ICU. Compared to associative models of AI, which develop rules based on finding associations in datasets, digital twin AI created by the DELPHI process are easily interpretable models based on a current understanding of underlying physiology., (© 2023. The Author(s).)

Preoperative pathogen identification in patients with periprosthetic joint infection (PJI) is typically limited to synovial fluid culture. Whether sequencing-based approaches are of potential use in identification of pathogens in PJI, and if so which approach is ideal, is incompletely defined. The objective of the study was to analyze the accuracy of a 16S rRNA (rRNA) gene-based PCR followed by Sanger sequencing and/or targeted metagenomic sequencing approach (tMGS) performed on synovial fluid for PJI diagnosis. A retrospective study was conducted, analyzing synovial fluids tested between August 2020 and May 2021 at a single center. Subjects with hip, knee, shoulder, and elbow arthroplasties who had synovial fluid aspirated and clinically subjected to sequence-based testing and conventional culture were studied. A total of 154 subjects were included in the study; 118 had noninfectious arthroplasty failure (NIAF), while 36 had PJI. Clinical sensitivity and specificity for diagnosis of PJI were 69% and 100%, respectively, for the sequencing-based approach and 72% and 100%, respectively, for conventional culture ( P  = 0.74). The combination of both tests was more sensitive (83%) than culture alone ( P  = 0.04). Results of sequencing-based testing led to changes in treatment in four of 36 (11%) PJI subjects. Microbial identification was achieved using Sanger and next generation sequencing in 19 and 6 subjects, respectively. When combined with culture, the described 16S rRNA gene sequencing-based approach increased sensitivity compared to culture alone, suggesting its potential use in the diagnosis of PJI when synovial fluid culture is negative. IMPORTANCE Periprosthetic joint infection (PJI) is a dreadful complication of joint replacement. Noninvasive identification of infectious pathogens has been traditionnally limited to culture-based testing of synovial fluid which has poor sensitivity. Sanger and Next-generation sequencing (NGS) may be used for synovial fluid testing in PJI, but experience in routine practice is sparse. We used a targeted metagenomic sequencing approach for routine testing of synovial fluid involving NGS when Sanger sequencing had failed or was likely to fail. The objective of this study was to analyze the approach's performance for diagnosis of PJI in comparison to culture for testing synovial fluid. Overall, the sequencing-based approach was not superior to culture for diagnosis of PJI, but yielded positive results in some culture-negative samples.

Initial microbiologic diagnosis of infective endocarditis (IE) relies on blood cultures and Bartonella and Coxiella burnetii serology. Small case series and one prospective study have preliminarily reported application of metagenomic sequencing on blood or plasma for IE diagnosis. Here, results of a prospective pilot study evaluating targeted metagenomic sequencing (tMGS) for blood-based early pathogen detection and identification in IE are reported. Subjects diagnosed with possible or definite IE at a single institution were prospectively enrolled with informed consent from October 2020 to July 2021. Blood was drawn and separated into whole blood and plasma. Both specimen types were subjected to nucleic acid extraction and PCR targeting the V1-V3 region of the 16S ribosomal RNA gene, followed by next-generation sequencing on an Illumina MiSeqTM platform. 35 subjects, 28 (80%) with definite and 7 (20%) with possible IE were enrolled, including 6 (17%) with blood culture-negative endocarditis (BCNE). Overall, 20 whole blood (59%) and 16 plasma (47%) samples tested positive ( P  = 0.47). When results of whole blood and plasma testing were combined, a positive tMGS result was found in 23 subjects (66%). tMGS identified a potential pathogen in 5 of 6 culture-negative IE cases. Although further study is needed, the results of this pilot study suggest that blood-based tMGS may provide pathogen identification in subjects with IE, including in culture-negative cases.

To date, no study has described the microbiological profile of surgical site infections (SSIs) after spine surgery in a tropical environment. The main objective of this study is to describe the microbiology and the risk factors of SSI after spinal surgery in a tropical climate. Our hypothesis is that the microbiology of SSIs in tropical areas is different to what is mainly described in temperate countries. As a consequence, the recommendation for antibiotic prophylaxis administered in the operative room, which mainly relays on the literature, might not be adequate in such countries. We included 323 consecutive patients who underwent a spinal intervention between 2017 and 2019, with a 2-year minimum follow-up. Objective ISO criteria were established in accordance with the criteria accepted by the Center of Disease Control in Atlanta. The identification of risk factors for SSI was carried out by uni- and multivariate analysis with a significance threshold of P < 0.05. The incidence of SSI was 7.7%. A total of 54.8% were in favor of a predominantly digestive origin of germs with an average of 1.68 bacteria found by ISO. Inadequate antibiotic prophylaxis was found in 54.8%. Age and body mass index were found to be independent risk factors for SSI. We report here an unusual microbiological profile of SSI with a predominance of gram-negative bacteria and a low proportion of Staphylococcus aureus and Staphylococcus epidermidis.

Central line-associated bloodstream infection (CLABSI) contributes to mortality and cost. While aseptic dressings and antibiotic-impregnated catheters prevent some extraluminal infections, intraluminal infections remain a source of CLABSIs. In this proof-of-concept study, an electrochemical intravascular catheter (e-catheter) prototype capable of electrochemically generating hypochlorous acid intraluminally using platinum electrodes polarized at a constant potential of 1.5 electrode potential relative to saturated silver/silver chloride reference electrode measured in volts (V Ag/AgCl ) was developed. After 24 h of prepolarization at 1.5 V Ag/AgCl , their activity was tested against clinical isolates of Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecium, and Escherichia coli derived from catheter-related infections. e-catheters generated a mean HOCl concentration of 15.86 ± 4.03 μM and had a mean pH of 6.14 ± 0.79. E-catheters prevented infections of all four species, with an average reduction of 8.41 ± 0.61 log 10 CFU/ml at 48 h compared to controls. Polarized e-catheters which generate low amounts of HOCl continuously should be further developed to prevent intraluminal infection. IMPORTANCE Catheter-related infections constitute an economic and mortality burden in health care. Several options are available to reduce the risk of infection, but only a few focus on preventing intraluminal infection, which occurs in long-term catheters, most often used for dialysis, prolonged treatment, or chemotherapy. A prototype of a catheter called an "e-catheter" composed of three electrodes, capable of producing hypochlorous acid (HOCl) electrochemically in its lumen, was developed. When polarized at 1.5 V, chloride ions in the solution are oxidized to continuously produce low amounts of HOCl, which exhibits antibacterial activity in the lumen of the catheter. Here, this prototype was shown to be able to generate HOCl as well as prevent infection in a preliminary in vitro catheter model. This approach is a potential strategy for catheter infection prevention.

Biofilms formed by antibiotic-resistant bacteria in wound beds present unique challenges in terms of treating chronic wound infections; biofilms formed by one or more than one bacterial species are often involved. In this work, the in vitro anti-biofilm activity of a novel electrochemical bandage (e-bandage) composed of carbon fabric and controlled by a wearable potentiostat, designed to continuously deliver low amounts of hydrogen peroxide (H 2 O 2 ) was evaluated against 34 mono-species and 12 dual-species membrane bacterial biofilms formed by Staphylococcus aureus , S. epidermidis , Enterococcus faecium , E. faecalis , Streptococcus mutans , Escherichia coli , Pseudomonas aeruginosa , Acinetobacter baumannii , Klebsiella pneumoniae , Cutibacterium acnes , and Bacteroides fragilis . Biofilms were grown on polycarbonate membranes placed atop agar plates. An e-bandage, which electrochemically reduces dissolved oxygen to H 2 O 2 when polarized at -0.6 V Ag/AgCl , was then placed atop each membrane biofilm and polarized continuously for 12, 24, and 48 h using a wearable potentiostat. Time-dependent decreases in viable CFU counts of all mono- and dual-species biofilms were observed after e-bandage treatment. 48 h of e-bandage treatment resulted in an average reduction of 8.17 ± 0.40 and 7.99 ± 0.32 log 10  CFU/cm 2 for mono- and dual-species biofilms, respectively. Results suggest that the described H 2 O 2 producing e-bandage can reduce in vitro viable cell counts of biofilms grown either in mono- or dual-species forms, and should be further developed as a potential antibiotic-free treatment strategy for treating chronic wound infections., Competing Interests: This research was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under the grant number R01 AI091594. The authors would like to thank Henry Chambers III (University of California, San Francisco) for providing S. aureus USA100, USA200, and USA300; Caliper Life Sciences for providing S. aureus Xen 30, S. epidermidis Xen 43, and P. aeruginosa Xen 5; Daniel Hassett (University of Cincinnati) for providing P. aeruginosa PAO1, PA14, and PA14 Δkat AB; and the Antibacterial Resistance Leadership Group (supported by a grant from the National Institutes of Health through Duke University) for providing A. baumannii ARLG-1268. R.P. reports grants from CD Diagnostics, Merck, Hutchison Biofilm Medical Solutions, Accelerate Diagnostics, ContraFect, TenNor Therapeutics Limited, and Shionogi. R.P. is a consultant for Curetis, Specific Technologies, Next Gen Diagnostics, PathoQuest, Selux Diagnostics, 1928 Diagnostics, and Qvella; monies are paid to Mayo Clinic. In addition, R.P. has patents on Bordetella pertussis/parapertussis PCR, a device/method for sonication with royalties paid by Samsung to Mayo Clinic, and an antibiofilm substance. R.P. receives travel reimbursement from ASM and IDSA, an editor's stipend from IDSA, and honoraria from the NBME, Up-to-Date, and the Infectious Diseases Board Review Course. H.B. holds a patent (US20180207301A1), “Electrochemical reduction or prevention of infections,” which refers to the electrochemical scaffold described herein., (© 2021 The Authors.)

Background: Choosing the right size of the stem is crucial for uncemented hip arthroplasty. Undersizing can lead to early loosening, peri-prosthetic fracture due to femoral implant insertion, and/or osteointegration failure. The main objective of this study was to find a correlation between the surgical approach and the intramedullary prosthetic canal fill ratio (CFR) of the uncemented femoral implant. The hypothesis of this work was that the surgical approach does not influence the stem sizing during hip arthroplasty., Methods: In this consecutive series, we analyzed the radiological images of 183 patients who underwent primary hip arthroplasty with 4 different surgical approaches. Dimensions of the implant were evaluated by radiographic measurement of the CFR. In order to assess the shape of the femur, we measured the canal flare index on the preoperative radiographs, and the canal calcar ratio was also measured to establish the shape of the femur according to Dorr's classification., Results: No significant difference was found between the surgical approach and the CFR measured at 4 different levels (CFR 1, 2, 3, and 4) on the postoperative radiograph. When the shape of the femur was assessed by canal flare index, there was no significant difference in implant, whether the femur had a stovepipe canal shape or a champagne-fluted canal shape., Conclusion: This study showed that the surgical approach in hip arthroplasty does not influence the canal fill. Therefore, the surgical approach does not factor in undersizing the femoral implant. Despite some difficulties in the exposure of the medullary shaft described by some authors, the anterior approach is not a risk factor for undersizing an anatomical femoral stem., Level of Evidence: 4., (© 2021 The Authors.)

Artificial intelligence (AI) and digital twin models of various systems have long been used in industry to test products quickly and efficiently. Use of digital twins in clinical medicine caught attention with the development of Archimedes, an AI model of diabetes, in 2003. More recently, AI models have been applied to the fields of cardiology, endocrinology, and undergraduate medical education. The use of digital twins and AI thus far has focused mainly on chronic disease management, their application in the field of critical care medicine remains much less explored. In neurocritical care, current AI technology focuses on interpreting electroencephalography, monitoring intracranial pressure, and prognosticating outcomes. AI models have been developed to interpret electroencephalograms by helping to annotate the tracings, detecting seizures, and identifying brain activation in unresponsive patients. In this mini-review we describe the challenges and opportunities in building an actionable AI model pertinent to neurocritical care that can be used to educate the newer generation of clinicians and augment clinical decision making., Competing Interests: Conflict-of-interest statement: All authors declare no conflict of interest., (©The Author(s) 2021. Published by Baishideng Publishing Group Inc. All rights reserved.)

Hydrogen peroxide (H 2 O 2 ) and hypochlorous acid (HOCl) are biocides used for cleaning and debriding chronic wound infections, which often harbor drug resistant bacteria. Here, we evaluated the in vitro activity of H 2 O 2 and HOCl against 27 isolates of eight bacterial species involved in wound infections. Minimum inhibitory concentrations (MICs) and minimum biofilm bactericidal concentrations (MBBCs) were measured. When compared to their respective MICs, MBBCs of isolates exposed to H 2 O 2 were 16- to 1,024-fold higher and those exposed to HOCl were 2- to 4-fold higher. We evaluated selection of resistance after exposure of Staphylococcus aureus and Pseudomonas aeruginosa biofilms to 10 iterations of electrochemically generated HOCl or H 2 O 2 delivered using electrochemical scaffolds (e-scaffolds), observing no decrease in anti-biofilm effects with serial exposure to e-scaffold-generated H 2 O 2 or HOCl. 24-hour exposure to H 2 O 2 -generating e-scaffolds consistently decreased colony forming units (CFUs) of S. aureus and P. aeruginosa biofilms by ∼5.0-log 10 and ∼4.78-log 10 through 10 iterations of exposure, respectively. 4-hour exposure to HOCl-generating e-scaffolds consistently decreased CFUs of S. aureus biofilms by ∼4.9-log 10 , and 1-hour exposure to HOCl-generating e-scaffolds consistently decreased CFUs of P. aeruginosa biofilms by ∼1.57-log 10 These results suggest that HOCl has similar activity against planktonic and biofilm bacteria, whereas the activity of H 2 O 2 is less against biofilm than planktonic bacteria, and that repeat exposure to either biocide, generated electrochemically under the experimental conditions studied, does not lessen antibiofilm effects., (Copyright © 2021 American Society for Microbiology.)

Oxidizing agents like hypochlorous acid (HOCl) have antimicrobial activity. We developed an integrated electrochemical scaffold, or e-scaffold, that delivers a continuous low dose of HOCl aimed at targeting microbial biofilms without exceeding concentrations toxic to humans as a prototype of a device being developed to treat wound infections in humans. In this work, we tested the device against 33 isolates of bacteria (including isolates with acquired antibiotic resistance) grown as in vitro biofilms alongside 12 combinations of dual-species in vitro biofilms. Biofilms were grown on the bottoms of 12-well plates for 24 h. An integrated e-scaffold was placed atop each biofilm and polarized at 1.5 V for 1, 2, or 4 h. HOCl was produced electrochemically by oxidizing chloride ions (Cl - ) in solution to chlorine (Cl 2 ); dissolved Cl 2 spontaneously dissociates in water to produce HOCl. The cumulative concentration of HOCl produced at the working electrode in each well was estimated to be 7.89, 13.46, and 29.50 mM after 1, 2, and 4 h of polarization, respectively. Four hours of polarization caused an average reduction of 6.13 log 10 CFU/cm 2 (±1.99 log 10 CFU/cm 2 ) of viable cell counts of monospecies biofilms and 5.53 log 10 CFU/cm 2 (±2.31 log 10 CFU/cm 2 ) for the 12 dual-species biofilms studied. The described integrated e-scaffold reduces viable bacterial cell counts in biofilms formed by an array of antibiotic-susceptible and -resistant bacteria alone and in combination., (Copyright © 2021 American Society for Microbiology.)

Hip dysplasia is an important cause of osteoarthritis in young adults. For these patients, conservative treatment is an interesting alternative to arthroplasty. The current literature suggests better clinical and functional outcomes when shelf acetabuloplasty is performed for a moderate joint pinch (<50%) associated with an important external coverage defect of the acetabular cup (<25°). Compared with open surgical procedures, minimally invasive surgical techniques or arthroscopy tend to reduce morbidity. To date, the major intraoperative difficulty remains the positioning of the graft. This Technical Note aims to outline a minimally invasive shelf acetabuloplasty, with optimization of the position of the autologous iliac crest bone graft using 3-dimensional navigation., (© 2020 by the Arthroscopy Association of North America. Published by Elsevier.)