Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2024 Update by the Infectious Diseases Society of America (IDSA) and the American Society for Microbiology (ASM).

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. This document, developed by experts in both adult and pediatric laboratory and clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. Sections are divided into anatomic systems, including Bloodstream Infections and Infections of the Cardiovascular System, Central Nervous System Infections, Ocular Infections, Soft Tissue Infections of the Head and Neck, Upper Respiratory Infections, Lower Respiratory Tract infections, Infections of the Gastrointestinal Tract, Intraabdominal Infections, Bone and Joint Infections, Urinary Tract Infections, Genital Infections, and Skin and Soft Tissue Infections; or into etiologic agent groups, including arboviral Infections, Viral Syndromes, and Blood and Tissue Parasite Infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also addressed. There is redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a reference to guide physicians in choosing tests that will aid them to diagnose infectious diseases in their patients.

Virtual multi-institutional tumor board: a strategy for personalized diagnoses and management of rare CNS tumors.

PURPOSE: Multidisciplinary tumor boards (MTBs) integrate clinical, molecular, and radiological information and facilitate coordination of neuro-oncology care. During the COVID-19 pandemic, our MTB transitioned to a virtual and multi-institutional format. We hypothesized that this expansion would allow expert review of challenging neuro-oncology cases and contribute to the care of patients with limited access to specialized centers. METHODS: We retrospectively reviewed records from virtual MTBs held between 04/2020-03/2021. Data collected included measures of potential clinical impact, including referrals to observational or therapeutic studies, referrals for specialized neuropathology analysis, and whether molecular findings led to a change in diagnosis and/or guided management suggestions. RESULTS: During 25 meetings, 32 presenters discussed 44 cases. Approximately half (n = 20; 48%) involved a rare central nervous system (CNS) tumor. In 21% (n = 9) the diagnosis was changed or refined based on molecular profiling obtained at the NIH and in 36% (n = 15) molecular findings guided management. Clinical trial suggestions were offered to 31% (n = 13), enrollment in the observational NCI Natural History Study to 21% (n = 9), neuropathology review and molecular testing at the NIH to 17% (n = 7), and all received management suggestions. CONCLUSION: Virtual multi-institutional MTBs enable remote expert review of CNS tumors. We propose them as a strategy to facilitate expert opinions from specialized centers, especially for rare CNS tumors, helping mitigate geographic barriers to patient care and serving as a pre-screening tool for studies. Advanced molecular testing is key to obtaining a precise diagnosis, discovering potentially actionable targets, and guiding management.

Next-Generation Sequencing Supports Targeted Antibiotic Treatment for Culture Negative Orthopedic Infections.

The isolation of an infective pathogen can be challenging in some patients with active, clinically apparent infectious diseases. Despite efforts in the microbiology lab to improve the sensitivity of culture in orthopedic implant-associated infections, the clinically relevant information often falls short of expectations. The management of peri-prosthetic joint infections (PJI) provides an excellent example of the use and benefits of newer diagnostic technologies to supplement the often-inadequate yield of traditional culture methods as a substantial percentage of orthopedic infections are culture-negative. Next-generation sequencing (NGS) has the potential to improve upon this yield. Bringing molecular diagnostics into practice can provide critical information about the nature of the infective organisms and allow targeted therapy in these otherwise challenging situations. This review article describes the current state of knowledge related to the use and potential of NGS to diagnose infections, particularly in the setting of PJIs.

Advances in Central Nervous System Tumor Classification.

Historically, the classification of tumors of the central nervous system (CNS) relies on the histologic appearance of cells under a microscope; however, the molecular era of medicine has resulted in new diagnostic paradigms anchored in the intrinsic biology of disease. The 2021 World Health Organization (WHO) reformulated the classification of CNS tumors to incorporate molecular parameters, in addition to histology, to define many tumor types. A contemporary classification system with integrated molecular features aims to provide an unbiased tool to define tumor subtype, the risk of tumor progression, and even the response to certain therapeutic agents. Meningiomas are heterogeneous tumors as depicted by the current 15 distinct variants defined by histology in the 2021 WHO classification, which also incorporated the first moelcular critiera for meningioma grading: homozygous loss of CDKN2A/B and TERT promoter mutation as criteria for a WHO grade 3 meningioma. The proper classification and clinical management of meningioma patients requires a multidisciplinary approach, which in addition to the information on microscopic (histology) and macroscopic (Simpson grade and imaging), should also include molecular alterations. In this chapter, we present the most up-to-date knowledge in CNS tumor classification, particularly in meningioma, in the molecular era and how it could affect their future classification and clinical management of patients with these diseases.

Clinical Laboratory Biosafety Gaps: Lessons Learned from Past Outbreaks Reveal a Path to a Safer Future.

Patient care and public health require timely, reliable laboratory testing. However, clinical laboratory professionals rarely know whether patient specimens contain infectious agents, making ensuring biosafety while performing testing procedures challenging. The importance of biosafety in clinical laboratories was highlighted during the 2014 Ebola outbreak, where concerns about biosafety resulted in delayed diagnoses and contributed to patient deaths. This review is a collaboration between subject matter experts from large and small laboratories and the federal government to evaluate the capability of clinical laboratories to manage biosafety risks and safely test patient specimens. We discuss the complexity of clinical laboratories, including anatomic pathology, and describe how applying current biosafety guidance may be difficult as these guidelines, largely based on practices in research laboratories, do not always correspond to the unique clinical laboratory environments and their specialized equipment and processes. We retrospectively describe the biosafety gaps and opportunities for improvement in the areas of risk assessment and management; automated and manual laboratory disciplines; specimen collection, processing, and storage; test utilization; equipment and instrumentation safety; disinfection practices; personal protective equipment; waste management; laboratory personnel training and competency assessment; accreditation processes; and ethical guidance. Also addressed are the unique biosafety challenges successfully handled by a Texas community hospital clinical laboratory that performed testing for patients with Ebola without a formal biocontainment unit. The gaps in knowledge and practices identified in previous and ongoing outbreaks demonstrate the need for collaborative, comprehensive solutions to improve clinical laboratory biosafety and to better combat future emerging infectious disease outbreaks.

First-Time Lumbar Medial Branch Radiofrequency Ablation: Patient-Reported Outcomes Measurement Information System as a Metric of Outcome.

OBJECTIVE: To investigate the ability of Patient-Reported Outcomes Measurement Information System (PROMIS) to capture the therapeutic effect of first-time medial branch radiofrequency ablation (RFA). DESIGN: Before-after trial. SETTING: Single academic spine center. PARTICIPANTS: Patients who underwent first-time medial branch RFA for lumbar facet joint pain identified by dual comparative medial branch block with ≥80% pain relief between January 1, 2015 and September 1, 2019 were identified using procedural billing codes. Charts were reviewed manually to confirm accuracy and strict adherence to the 80% pain relief threshold for each medial branch block. Thirty-nine patients met the criteria and were included in this study (N=39). INTERVENTIONS: Medial branch RFA. MAIN OUTCOME MEASURES: PROMIS score domains of Depression, Pain Interference, and Physical Function collected pre- and post RFA were compared. Pretreatment scores were within 6 weeks prior to the first medial branch block. Posttreatment scores were between 5 weeks and 6 months after RFA. Paired-sample t test analyses were used to calculate responsiveness to treatment, with significance assigned as P<.05 prior to acquiring data. Effect size was calculated using Cohen's d. RESULTS: PROMIS domains of Pain Interference and Physical Function demonstrated a statistically significant improvement (P=.004 and P=.017, respectively). The PROMIS domain of Depression did not demonstrate a statistically significant change (P=.12). The effect size was medium (d=-0.43) for Pain Interference, small/medium (d=0.31) for Physical Function, and small (d=-0.12) for Depression. CONCLUSIONS: Medial branch RFA as a treatment for lumbar facet syndrome is associated with a statistical improvement in PROMIS domains of Physical Function and Pain Interference.

Digital imaging for reading of direct rapid antibiotic susceptibility tests from positive blood cultures.

Delaying effective antibiotic therapy is a major cause of sepsis-associated mortality. The EUCAST rapid antibiotic susceptibility test (RAST) is performed from positive blood cultures to provide rapid results. Disc diffusion tests inoculated with positive blood culture broth are read at 4, 6, and 8 h and interpreted against species and time-specific criteria. Potential problems are the possibility of missing specific reading times for tests and slower growth in incubators that are frequently opened. The current study aimed to assess if digital visualization by the BD Kiestra™ total laboratory automation system is suitable for reading RASTs by capturing images at the correct times and retaining them for review. Utilizing the Kiestra™ InoqulA, 100 µl of positive blood culture broth was lawn-inoculated onto Mueller-Hinton agar and incubated at 35 °C for automated digital zone measurement at 4, 6, and 8 h. Aliquots from 135 positive blood cultures were tested against EUCAST-recommended and other drugs and assessed for readability of digital images. Microdilution MICs were determined in parallel to RASTs. All isolates except 7/10 enterococci yielded images of suitable quality for zone measurement. Of the 641 digitally read tests for other organisms, 207 (32.3%) were readable in 4 h, 555 (86.6%) in 6 h, and 641 (100%) in 8 h. For tests included in EUCAST criteria, 92.1% provided categorical agreement with microdilution MICs. Digital image reading of RASTs is a potentially viable, inexpensive tool for providing rapid susceptibility results which can help reduce sepsis-associated mortality.

A Laboratory Medicine Best Practices Systematic Review and Meta-analysis of Nucleic Acid Amplification Tests (NAATs) and Algorithms Including NAATs for the Diagnosis of Clostridioides (Clostridium) difficile in Adults.

The evidence base for the optimal laboratory diagnosis of Clostridioides (Clostridium) difficile in adults is currently unresolved due to the uncertain performance characteristics and various combinations of tests. This systematic review evaluates the diagnostic accuracy of laboratory testing algorithms that include nucleic acid amplification tests (NAATs) to detect the presence of C. difficile The systematic review and meta-analysis included eligible studies (those that had PICO [population, intervention, comparison, outcome] elements) that assessed the diagnostic accuracy of NAAT alone or following glutamate dehydrogenase (GDH) enzyme immunoassays (EIAs) or GDH EIAs plus C. difficile toxin EIAs (toxin). The diagnostic yield of NAAT for repeat testing after an initial negative result was also assessed. Two hundred thirty-eight studies met inclusion criteria. Seventy-two of these studies had sufficient data for meta-analysis. The strength of evidence ranged from high to insufficient. The uses of NAAT only, GDH-positive EIA followed by NAAT, and GDH-positive/toxin-negative EIA followed by NAAT are all recommended as American Society for Microbiology (ASM) best practices for the detection of the C. difficile toxin gene or organism. Meta-analysis of published evidence supports the use of testing algorithms that use NAAT alone or in combination with GDH or GDH plus toxin EIA to detect the presence of C. difficile in adults. There is insufficient evidence to recommend against repeat testing of the sample using NAAT after an initial negative result due to a lack of evidence of harm (i.e., financial, length of stay, or delay of treatment) as specified by the Laboratory Medicine Best Practices (LMBP) systematic review method in making such an assessment. Findings from this systematic review provide clarity to diagnostic testing strategies and highlight gaps, such as low numbers of GDH/toxin/PCR studies, in existing evidence on diagnostic performance, which can be used to guide future clinical research studies.

Randomized prospective trial of fractionated stereotactic radiosurgery with chemotherapy versus chemotherapy alone for bevacizumab-resistant high-grade glioma.

PURPOSE: Outcomes for patients with recurrent high-grade glioma (HGG) progressing on bevacizumab (BEV) are dismal. Fractionated stereotactic radiosurgery (FSRS) has been shown to be feasible and safe when delivered in this setting, but prospective evidence is lacking. This single-institution randomized trial compared FSRS plus BEV-based chemotherapy versus BEV-based chemotherapy alone for BEV-resistant recurrent malignant glioma. MATERIALS AND METHODS: HGG patients on BEV with tumor progression after 2 previous treatments were randomized to 1) FSRS plus BEV-based chemotherapy or 2) BEV-based chemotherapy with irinotecan, etoposide, temozolomide, or carboplatin. FSRS was delivered as 32 Gy (8 Gy × 4 fractions within 2 weeks) to the gross target volume and 24 Gy (6 Gy × 4 fractions) to the clinical target volume (fluid-attenuated inversion recovery abnormality). The primary endpoints were local control (LC) at 2 months and progression-free survival (PFS). RESULTS: Of the 35 patients enrolled, 29 had glioblastoma (WHO IV) and 6 had anaplastic glioma (WHO III). The median number of prior recurrences was 3. Patients treated with FSRS had significantly improved PFS (5.1 vs 1.8 months, P < .001) and improved LC at 2 months (82% [14/17] vs 27% [4/15], P = .002). The overall median survival was 6.6 months (7.2 months with FSRS vs 4.8 months with chemotherapy alone, P = .11). CONCLUSIONS: FSRS combined with BEV-based chemotherapy in recurrent HGG patients progressing on BEV is feasible and improves LC and PFS when compared to treatment with BEV-based chemotherapy alone.

Developing Real-world Evidence-Ready Datasets: Time for Clinician Engagement.

PURPOSE OF REVIEW: Real-world data (RWD) applications in healthcare that support learning health systems and pragmatic clinical trials are gaining momentum, largely due to legislation supporting real-world evidence (RWE) for drug approvals. Clinical notes are thought to be the cornerstone of RWD applications, particularly for conditions with limited effective treatments, extrapolation of treatments from other conditions, or heterogenous disease biology and clinical phenotypes. RECENT FINDINGS: Here, we discuss current issues in applying RWD captured at the point-of-care and provide a framework for clinicians to engage in RWD collection. To achieve clinically meaningful results, RWD must be reliably captured using consistent terminology in the description of our patients. RWD complements traditional clinical trials and research by informing the generalizability of results, generating new hypotheses, and creating a large data network for scientific discovery. Effective clinician engagement in the development of RWD applications is necessary for continued progress in the field.

Effect of seizure timing on long-term survival in patients with brain tumor.

OBJECTIVE: Seizures often occur in patients with primary brain tumor (BT). The aim of this study was to determine if there is an association between the time of occurrence of seizures during the course of BT and survival of these patients. METHODS: This retrospective cohort study at Henry Ford Hospital, an urban tertiary referral center, included all patients who were diagnosed with primary BTs at Henry Ford Health System between January 2006 and December 2014. Timing of seizure occurrence, if occurred at presentation or after the tumor diagnosis during follow-up period, in different grades of BTs, and survival of these patients were analyzed. RESULTS: Of the 901 identified patients, 662 (53% male; mean age: 56 years) were included in final analysis, and seizures occurred in 283 patients (43%). Patients with World Health Organization (WHO) grade III BT with seizures as a presenting symptom only had better survival (adjusted hazard ratio (HR): 0.27; 95% confidence interval (CI), 0.11-0.67; P = 0.004). Seizures that occurred after tumor diagnosis only (adjusted HR: 2.11; 95% CI, 1.59-2.81; P < 0.001) in patients with WHO grade II tumors (adjusted HR: 3.41; 95% CI, 1.05-11.1; P = 0.041) and WHO grade IV tumors (adjusted HR: 2.14; 95% CI, 1.58-2.90; P < 0.001) had higher mortality. Seizures that occurred at presentation and after diagnosis also had higher mortality (adjusted HR: 1.34; 95% CI, 1.00-1.80; P = 0.049), in patients with meningioma (adjusted HR: 6.19; 95% CI, 1.30-29.4; P = 0.021) and grade III tumors (adjusted HR: 6.19; 95% CI, 2.56-15.0; P < 0.001). CONCLUSION: Seizures occurred in almost half of the patients with BTs. The association between seizures in patients with BT and their survival depends on the time of occurrence of seizures, if occurring at presentation or after tumor diagnosis, and the type of tumor. Better survival was noted in patients with WHO grade III BTs who had seizures at presentation at the time of diagnosis, while higher mortality was noted in WHO grade II tumors who had seizure at presentation and after tumor diagnosis, and in grade IV tumors after tumor diagnosis.

TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units.

Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem's speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. This greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.

Baseline nocturnal glucose change: A predictor of the treatment effect of bolus intensification in insulin-treated type 2 diabetes.

This post hoc analysis of an 18-week randomized trial explored the utility of calculating baseline glycated haemoglobin (HbA1c), postprandial glucose (PPG) increments and nocturnal glucose change in predicting efficacy and safety outcomes in response to bolus insulin intensification in people with type 2 diabetes (T2D). Analyses were conducted on 236 participants with T2D receiving metformin: 116 received fast-acting insulin aspart (faster aspart) basal-bolus therapy and 120 received basal-only insulin. Participants were grouped according to baseline HbA1c, PPG increments and nocturnal glucose change variables; analyses were performed on the end-of-trial treatment differences between "high" and "low" baseline values. The change from baseline in end-of-trial mean HbA1c and mean PPG increments was in favour of faster aspart across all subgroups. Significantly greater treatment differences were observed in participants with high (vs. low) baseline nocturnal glucose change and PPG increments. For baseline HbA1c, significantly greater treatment differences were observed for change in end-of-trial PPG increments, but not end-of-trial HbA1c. In conclusion, both nocturnal glucose change and PPG increments may be more useful than HbA1c for identifying subgroups of people with T2D who would most benefit from bolus intensification.

Percutaneous Costoclavicular Bypass for Thoracic Outlet Syndrome and Cephalic Arch Occlusion in Hemodialysis Patients.

PURPOSE: To report results of percutaneous costoclavicular bypass for symptomatic thoracic outlet or cephalic arch occlusion in patients with arteriovenous fistula. MATERIALS AND METHODS: A retrospective review of percutaneous costoclavicular bypass patients between 2014 and 2018 was performed. Stent grafts were placed subcutaneously over the clavicle from the fistula outflow (axillary or cephalic vein) into a jugular vein or collateral. The procedures were performed in patients who had exhausted or were not candidates for balloon dilation or intravascular stent placement. RESULTS: Technical success was 100% (9/9) with resolution of symptoms in all patients. Indications were arm swelling in 67% (6/9), fistula dysfunction in 22% (2/7), and 1 enlarging aneurysm. The fistula outflow was cephalic in 67% (6/9) and axillary in 33% (3/9). The return vessel was external jugular in 78% (7/9) and internal jugular in 22% (2/9). Two overlapping Viabahn stent grafts were used in 88% of cases (7/8) and 3 stent grafts in 1 case. In the initial case, 2 Gore hybrid grafts were used. Stent graft diameter ranged from 9 mm to 13 mm. Mean follow-up was 852 ± 339 days (range, 488-1483 days). At 12 months and 24 months, primary patency was 67% and 67%, and secondary patency was 89% and 78%, respectively. Complications included late thrombosis and secondary infection. There were no anastomotic leaks or seromas associated with extravascular stent grafts. CONCLUSIONS: The percutaneous costoclavicular bypass is a feasible option for thoracic outlet and cephalic arch occlusion in symptomatic dialysis patients.

Effects of the After Deployment: Adaptive Parenting Tools (ADAPT) intervention on fathers and their children: A moderated mediation model.

Deployment to war is associated with disruptions to emotion regulation and parenting. Using data from a randomized controlled trial, we examined whether fathers with poorer emotion regulation would differentially benefit from the After Deployment, Adaptive Parenting Tools program, a 14-session group-based parenting intervention. Prior analyses of the intervention demonstrated benefits to observed couple parenting and children's adjustment, but not to fathers' observed parenting. In this study we examined whether intervention effects on fathers' observed distress avoidance were moderated by baseline emotion regulation, and whether reduced distress avoidance was associated with improved observed parenting and reduced children's internalizing symptoms. A subset of the full randomized controlled trial sample (181 families with a father who had returned from deployment to war in Iraq or Afghanistan, a nondeployed mother, and a target child aged 4-13) completed measures at baseline, 12-months, and 24-months postbaseline. Results indicated that fathers high in baseline emotion regulation difficulties assigned to the intervention group showed reductions in observed distress avoidance at 12 months compared to controls, which were subsequently associated with improvements in observed parenting practices and reductions in children's internalizing symptoms at 24 months. The results suggest a role for personalizing parenting programs for fathers high in emotion dysregulation.

Common variants at 5q33.1 predispose to migraine in African-American children.

BACKGROUND: Genome-wide association studies (GWASs) have identified multiple susceptibility loci for migraine in European adults. However, no large-scale genetic studies have been performed in children or African Americans with migraine. METHODS: We conducted a GWAS of 380 African-American children and 2129 ancestry-matched controls to identify variants associated with migraine. We then attempted to replicate our primary analysis in an independent cohort of 233 African-American patients and 4038 non-migraine control subjects. RESULTS: The results of this study indicate that common variants at 5q33.1 associated with migraine risk in African-American children (rs72793414, p=1.94×10-9). The association was validated in an independent study (p=3.87×10-3) for an overall meta-analysis p value of 3.81×10-10. eQTL (Expression quantitative trait loci) analysis of the Genotype-Tissue Expression data also shows the genotypes of rs72793414 were strongly correlated with the mRNA expression levels of NMUR2 at 5q33.1. NMUR2 encodes a G protein-coupled receptor of neuromedin-U (NMU). NMU, a highly conserved neuropeptide, participates in diverse physiological processes of the central nervous system. CONCLUSIONS: This study provides new insights into the genetic basis of childhood migraine and allow for precision therapeutic development strategies targeting migraine patients of African-American ancestry.

Intraclass Correlations of Measured Magnetic Resonance Imaging Volumes of Laser Interstitial Thermal Therapy-Treated High-Grade Gliomas.

BACKGROUND AND OBJECTIVES: Laser interstitial thermal therapy (LITT) is a minimally invasive therapeutic option for the treatment of brain tumors. Previous studies have quantitatively followed the ablated volumes of high-grade gliomas. Reported treatment volumes range from 28% to 100%, with no reported interobserver analysis. Because these volumes are subjectively measured, it is necessary to establish concordance between clinicians. STUDY DESIGN/MATERIALS AND METHODS: Utilizing Brainlab tumor analysis software (Brainlab, Munich, Germany), five physician users traced out tumor volumes slice-by-slice on 10 treated tumors in eight patients. The participants were briefed with specific instructions and a demonstration on how to trace the enhancing borders of the tumor slice-by-slice. Volumes automatically calculated by the Brainlab software included preoperative, intraoperative ablation and postoperative enhancing volumes. Data regarding size, cystic appearance, pathology, previous surgery, and demographics were included. RESULTS: The intraclass correlation coefficient (ICC) for preoperative, intraoperative, and postoperative volumes was 0.92 (95% confidence interval, [CI] 0.81-0.97), 0.90 (0.77-0.96), and 0.89 (0.74-0.96), respectively. The overall ICC was 0.72 (0.50-0.87). ICC comparisons were also made for each pair of readers (neuroradiologist, neuro-oncologist, senior neurosurgery resident, neurosurgery junior resident) which resulted in pretreatment ICC scores of 0.97, 0.91, 0.66, 0.94; intratreatment scores of 0.97, 0.78, 0.90, 0.96; and posttreatment scores of 0.96, 0.81, 0.89, and 0.87. A Bland-Altman plot was also used to assess the differences in volumes. CONCLUSIONS: The ICC gives a composite of the consistency of measurements made by multiple observers measuring the same quantity. The overall ICC of 0.72 means there is good correlation between observers in our study between measured volumes. Lasers Surg. Med. © 2019 Wiley Periodicals, Inc.

The GluN2B-Glu413Gly NMDA receptor variant arising from a de novo GRIN2B mutation promotes ligand-unbinding and domain opening.

N-methyl-D-aspartate (NMDA) receptors are transmembrane glutamate-binding ion channels that mediate neurotransmission in mammals. NMDA receptor subunits are tetrameric complexes of GluN1 and GluN2A-D subunits, encoded by the GRIN gene family. Of these subunits, GluN2B is suggested to be required for normal development of the central nervous system. A mutation identified in a patient with developmental delay, E413G, resides in the GluN2B ligand-binding domain and substantially reduces glutamate potency by an unknown mechanism. GluN2B Gly413, though near the agonist, is not in van der Waals contact with glutamate. Visual analysis of the GluN2B structure with the E413G mutation modeled suggests that replacement of Glu with Gly at this position increases solvent access to the ligand-binding domain. This was confirmed by molecular modeling, which showed that the ligand is more mobile in GluN2B-E413G than WT GluN2B. Evaluation of agonist occupancy using random accelerated molecular dynamics (RAMD) simulations predicts that the glutamate exits the binding-site more rapidly for GluN2B-E413G than WT receptors. This analysis was extended to other binding-site mutations, which produced qualitative agreement between experimentally determined EC50 values, deactivation time constants, and ligand motion within the binding-site. Furthermore, long sub-microsecond molecular dynamics simulations of the bi-lobed ligand-binding domain revealed that it adopted a cleft-open ligand-free state more often for GluN2B-E413G than wild-type GluN2B. This is consistent with the idea that L-glutamate binding is altered such that the ligand-binding domain occupies the open-cleft conformation associated with the closed channel.

A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology.

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. This document presents a system-based approach rather than specimen-based approach, and includes bloodstream and cardiovascular system infections, central nervous system infections, ocular infections, soft tissue infections of the head and neck, upper and lower respiratory infections, infections of the gastrointestinal tract, intra-abdominal infections, bone and joint infections, urinary tract infections, genital infections, and other skin and soft tissue infections; or into etiologic agent groups, including arthropod-borne infections, viral syndromes, and blood and tissue parasite infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also emphasized. There is intentional redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a guidance for physicians in choosing tests that will aid them to quickly and accurately diagnose infectious diseases in their patients.

A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology.

The critical nature of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician/advanced practice provider and the microbiologists who provide enormous value to the healthcare team. This document, developed by experts in laboratory and adult and pediatric clinical medicine, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. This document presents a system-based approach rather than specimen-based approach, and includes bloodstream and cardiovascular system infections, central nervous system infections, ocular infections, soft tissue infections of the head and neck, upper and lower respiratory infections, infections of the gastrointestinal tract, intra-abdominal infections, bone and joint infections, urinary tract infections, genital infections, and other skin and soft tissue infections; or into etiologic agent groups, including arthropod-borne infections, viral syndromes, and blood and tissue parasite infections. Each section contains introductory concepts, a summary of key points, and detailed tables that list suspected agents; the most reliable tests to order; the samples (and volumes) to collect in order of preference; specimen transport devices, procedures, times, and temperatures; and detailed notes on specific issues regarding the test methods, such as when tests are likely to require a specialized laboratory or have prolonged turnaround times. In addition, the pediatric needs of specimen management are also emphasized. There is intentional redundancy among the tables and sections, as many agents and assay choices overlap. The document is intended to serve as a guidance for physicians in choosing tests that will aid them to quickly and accurately diagnose infectious diseases in their patients.