Culture-independent identification of bloodstream infections from whole blood: prospective evaluation in specimens of known infection status.

Sepsis caused by bloodstream infection (BSI) is a major healthcare burden and a leading cause of morbidity and mortality worldwide. Timely diagnosis is critical to optimize clinical outcome, as mortality rates rise every hour treatment is delayed. Blood culture remains the "gold standard" for diagnosis but is limited by its long turnaround time (1-7 days depending on the organism) and its potential to provide false-negative results due to interference by antimicrobial therapy or the presence of mixed (i.e., polymicrobial) infections. In this paper, we evaluated the performance of resistance and pathogen ID/BSI, a direct-from-specimen molecular assay. To reduce the false-positivity rate common with molecular methods, this assay isolates and detects genomic material only from viable microorganisms in the blood by incorporating a novel precursor step to selectively lyse host and non-viable microbial cells and remove cell-free genomic material prior to lysis and analysis of microbial cells. Here, we demonstrate that the assay is free of interference from host immune cells and common antimicrobial agents at elevated concentrations. We also demonstrate the accuracy of this technology in a prospective cohort pilot study of individuals with known sepsis/BSI status, including samples from both positive and negative individuals. IMPORTANCE: Blood culture remains the "gold standard" for the diagnosis of sepsis/bloodstream infection (BSI) but has many limitations which may lead to a delay in appropriate and accurate treatment in patients. Molecular diagnostic methods have the potential for markedly improving the management of such patients through faster turnaround times and increased accuracy. But molecular diagnostic methods have not been widely adopted for the identification of BSIs. By incorporating a precursor step of selective lysis of host and non-viable microorganisms, our resistance and pathogen ID (RaPID)/BSI molecular assay addresses many limitations of blood culture and other molecular assay. The RaPID/BSI assay has an approximate turnaround time of 4 hours, thereby significantly reducing the time to appropriate and accurate diagnosis of causative microorganisms in such patients. The short turnaround time also allows for close to real-time tracking of pathogenic clearance of microorganisms from the blood of these patients or if a change of antimicrobial regimen is required. Thus, the RaPID/BSI molecular assay helps with optimization of antimicrobial stewardship; prompt and accurate diagnosis of sepsis/BSI could help target timely treatment and reduce mortality and morbidity in such patients.

Extremal Kerr Black Holes as Amplifiers of New Physics.

We show that extremal Kerr black holes are sensitive probes of new physics. Stringy or quantum corrections to general relativity are expected to generate higher-curvature terms in the gravitational action. We show that in the presence of these terms, asymptotically flat extremal rotating black holes have curvature singularities on their horizon. Furthermore, near-extremal black holes can have large yet finite tidal forces for infalling observers. In addition, we consider five-dimensional extremal charged black holes and show that higher-curvature terms can have a large effect on the horizon geometry.

Current Issues in Blood Gas Analysis.

BACKGROUND: Blood gas analysis constitutes one of the most widely used tests, especially in critical care settings such as intensive care units, emergency departments, and operating rooms. Blood gas results are key for assessing acid-base balance and ventilatory control in critically ill patients. Because blood gas analysis plays a vital role in management of critically ill patients, this testing is frequently conducted at the point-of-care by users with various educational backgrounds across different hospital departments. CONTENT: When performing blood gas analysis, it is important to be aware of the analytical issues that may affect the different components of this testing. With blood gas analysis, differences in test names and method changes over time have led to several controversies that might affect test result interpretations. Hence, being aware of these controversies is important in ensuring appropriateness of result interpretations. Many blood gas testing programs face challenges with maintaining quality assurance. Having practical approaches to method verification, and choosing the right blood gas analyzer type, will go a long way to ensure quality in blood gas analysis. SUMMARY: We review analytical issues and controversies associated with blood gas testing, as well as practical approaches to deciding on a blood gas analyzer and quality assurance.

Medical appropriateness and economics of nucleic acid amplification testing for infectious diseases.

It has become commonplace to assume that nucleic acid amplification tests (NAATs) represent the gold standard for all infectious disease diagnostic testing. This proposition has become increasingly entrenched recently, as these tests can now be done, in comparison to even just a few years ago, relatively inexpensively and with rapid analytic turnaround times. Many can even be performed at the point of care by individuals without technical backgrounds. But there may be a dark underside to this proposition. Could these tests be too sensitive? Are they always "fit for purpose"? Should they trump clinical judgement? Do they have untoward impacts on antimicrobial therapy? Could the profit motive - by manufacturers and by laboratories - be fueling the explosive expansion of NAATs? In this article, we will explore these questions in regard to several specific NAAT examples - Group A Streptococcus, Influenza, SARS-CoV-2, respiratory panels, and sexually transmitted disease panels.

Clinical Diagnostic Point-of-Care Molecular Assays for SARS-CoV-2.

Laboratories faced many challenges throughout the COVID-19 pandemic. Point-of-care (POC) SARS-CoV-2 nucleic acid amplification tests (NAATs) provided a key solution to the need for rapid turnaround time in select patient populations and were implemented at the POC but also within laboratories to supplement traditional molecular assays. Clinical Laboratory Improvement Amendments-waived rapid POC SARS-CoV-2 NAATs offer the benefit of reduced educational requirements for operators and can be performed by non-laboratory-trained individuals. However, these methods must be validated to ensure the manufacturer's performance specifications are met and they are found to be fit-for-purpose in the clinical workflows they are implemented.

National Kidney Foundation Laboratory Engagement Working Group Recommendations for Implementing the CKD-EPI 2021 Race-Free Equations for Estimated Glomerular Filtration Rate: Practical Guidance for Clinical Laboratories.

Recognizing that race is a social and not a biological construct, healthcare professionals and the public have called for removal of race in clinical algorithms. In response, the National Kidney Foundation and the American Society of Nephrology created the Task Force on Reassessing the Inclusion of Race in Diagnosing Kidney Diseases to examine the issue and provide recommendations. The final report from the Task Force recommends calculating estimated glomerular filtration rate (eGFR) without a race coefficient using the recently published CKD-EPI 2021 creatinine (cr) and creatinine-cystatin C (cr-cys) equations. The Task Force recommends immediately replacing older eGFRcr equations (MDRD Study and CKD-EPI 2009) with the new CKD-EPI 2021 equation. In a 2019 survey by the College of American Pathologists, 23% of 6200 laboratories reporting eGFRcr used an incorrect equation that is not suitable for use with standardized creatinine measurements, 34% used the CKD-EPI 2009 equation and 43% used the MDRD Study 2006 equation re-expressed for standardized creatinine measurement. Rapid transition to using the CKD-EPI 2021 equation is an opportunity for laboratories to standardize to a single equation to eliminate differences in eGFRcr due to different equations used by different laboratories, and to report eGFR without use of race. We provide guidance to laboratories for implementing the CKD-EPI 2021 equations for both eGFRcr and eGFRcr-cys.

Boundary Causality Violating Metrics in Holography.

Even for holographic theories that obey boundary causality, the full bulk Lorentzian path integral includes metrics that violate this condition. This leads to the following puzzle: the commutator of two field theory operators at space-like-separated points on the boundary must vanish. However, if these points are causally related in a bulk metric, then the bulk calculation of the commutator will be nonzero. It would appear that the integral over all metrics of this commutator must vanish exactly for holography to hold. This is puzzling since it must also be true if the commutator is multiplied by any other operator. Upon a careful treatment of boundary conditions in holography, we show how the bulk path integral leads to a natural resolution of this puzzle.

Rapid detection and identification of bacteria directly from whole blood with light scattering spectroscopy based biosensor.

Bacterial infections are one of the major causes of death worldwide. The identification of a bacterial species that is the source of an infection generally takes a long time, and often exceeds the treatment window for seriously ill patients. Many of these deaths are preventable if the bacterial species can be identified quickly. Here we present an optical spectroscopic method for rapid detection and identification of bacteria directly from whole blood using a light scattering spectroscopy technique. This technique was originally developed to detect pre-cancerous changes in epithelial tissues, characterize changes in tissue on the cellular scale, and characterize biological structures comparable to or smaller than a single wavelength. We demonstrate here that not only can an inexpensive light scattering spectroscopy-based biosensor rapidly detect and identify four bacteria species in the blood, responsible for the majority of death causing infections, but that species-level identification can potentially be made based on approximately one thousand bacterial cells per milliliter of blood. Observing entire colonies or performing susceptibility testing is therefore not required.

Analytic Sensitivity of 3 Nucleic Acid Detection Assays in Diagnosis of SARS-CoV-2 Infection.

BACKGROUND: Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by reverse transcription PCR is the primary method to diagnose coronavirus disease 2019 (COVID-19). However, the analytic sensitivity required is not well defined and it is unclear how available assays compare. METHODS: For the Abbott RealTime SARS-CoV-2 assay (m2000; Abbott Molecular), we determined that it could detect viral concentrations as low as 26 copies/mL, we defined the relationship between cycle number and viral concentrations, and we tested naso- and oropharyngeal swab specimens from 8538 consecutive individuals. Using the m2000 as a reference assay method, we described the distribution of viral concentrations in these patients. We then used selected clinical specimens to determine the positive percent agreement of 2 other assays with more rapid turnaround times [Cepheid Xpert Xpress (GeneXpert; Cepheid); n = 27] and a laboratory developed test on the Luminex ARIES system [ARIES LDT (Luminex); n = 50] as a function of virus concentrations, from which we projected their false-negative rates in our patient population. RESULTS: SARS-CoV-2 was detected in 27% (95% CI: 26%-28%) of all specimens. Estimated viral concentrations were widely distributed, and 17% (95% CI: 16%-19%) of positive individuals had viral concentrations <845 copies/mL. Positive percent agreement was strongly related to viral concentration, and reliable detection (i.e., ≥95%) was observed at concentrations >100 copies/mL for the GeneXpert but not the ARIES LDT, corresponding to projected false-negative rates of 4% (95% CI: 0%-21%) and 27% (95% CI: 11%-46%), respectively. CONCLUSIONS: Substantial proportions of clinical specimens have low to moderate viral concentrations and may be missed by methods with less analytic sensitivity.

Accuracy-Based Vitamin D Survey: Six Years of Quality Improvement Guided by Proficiency Testing.

CONTEXT.­: The goal of the College of American Pathologists Accuracy-Based Proficiency Testing Program is to promote the quality, standardization, and harmonization of clinical laboratory results through proficiency testing specimens that are free from matrix effects, have target values that are traceable to reference methods, and that probe the limitations of current methods. OBJECTIVE.­: To summarize the first 6 years of the Accuracy-Based Vitamin D Survey and highlight key insights from the data generated as it relates to assay performance. DESIGN.­: Accuracy-based challenges were created by using pooled human serum samples. Certain samples were derived from participants in an institutional review board-approved protocol in which vitamin D-deficient participants were treated with ergocalciferol (vitamin D2). Reference targets for the survey were set by the Centers for Disease Control and Prevention using isotope-dilution liquid chromatography-tandem mass spectrometry. Each method was compared with the reference method procedure over the course of the program (n = 43 proficiency testing samples). RESULTS.­: Linear regression versus the reference method procedure revealed proportional biases across the methods, ranging from 0.0% to 16.7%. Pearson correlation coefficients (r2) ranged from 0.902 to 0.996. Results were influenced by the concentration of 25-hydroxyvitamin D2 as well as the C-3 epimer of 25-hydroxyvitamin D3. During the 6 years, 2 manufacturers altered their assays to match the reference method procedure more closely. CONCLUSIONS.­: There is considerable bias, both proportional bias and sample-specific matrix effects, affecting many assays. This ongoing accuracy-based proficiency testing program for vitamin D will provide the data needed for laboratories and manufacturers to improve their assays and thereby patient care.

Picoanalysis of Drugs in Biofluids with Quantitative Label-Free Surface-Enhanced Raman Spectroscopy.

The enormous increase of Raman signal in the vicinity of metal nanoparticles allows surface-enhanced Raman spectroscopy (SERS) to be employed for label-free detection of substances at extremely low concentrations. However, the ultimate potential of label-free SERS to identify pharmaceutical compounds at low concentrations, especially in relation to biofluid sensing, is far from being fully realized. Opioids are a particular challenge for rapid clinical identification because their molecular structural similarities prevent their differentiation with immunolabeling approaches. In this paper, a new method called quantitative label-free SERS (QLF-SERS) which involves the formation of halide-conjugated gold nanoclusters trapping the analyte of interest near the SERS hot spots is reported, and it is demonstrated that it yields a 105 fold improvement in the detection limit over previously reported results for the entire class of clinically relevant opioids and their metabolites. Measurements of opioid concentrations in multicomponent mixtures are also demonstrated. QLF-SERS has comparable detection limits as currently existing laboratory urine drug testing techniques but is significantly faster and inexpensive and, therefore, can be easily adapted as part of a rapid clinical laboratory routine.

Label-free spectrochemical probe for determination of hemoglobin glycation in clinical blood samples.

Glycated hemoglobin, HbA1c, is an important biomarker that reveals the average value of blood glucose over the preceding 3 months. While significant recent attention has been focused on the use of optical and direct molecular spectroscopic methods for determination of HbA1c, a facile test that minimizes sample preparation needs and turnaround time still remains elusive. Here, we report a label-free approach for identifying low, mid and high-HbA1c groups in hemolysate and in whole blood samples featuring resonance Raman (RR) spectroscopy and support vector machine (SVM)-based classification of spectral patterns. The diagnostic power of RR measurements stems from its selective enhancement of hemoglobin-specific features, which simultaneously minimizes the blood matrix spectral interference and permits detection in the native solution. In this pilot study, our spectroscopic observations reveal that glycation of hemoglobin results in subtle but reproducible changes even when detected in the whole blood matrix. Leveraging SVM analysis of the principal component scores determined from the RR spectra, we show high degree of accuracy in classifying clinical specimen. We envisage that the promising findings will pave the way for more extensive clinical specimen investigations with the ultimate goal of translating molecular spectroscopy for routine point-of-care testing.

Use of an electronic medical record reminder improves HIV screening.

BACKGROUND: More than 1 in 7 patients with human immunodeficiency virus (HIV) infection in the United States are unaware of their serostatus despite recommendations of US agencies that all adults through age 65 be screened for HIV at least once. To facilitate universal screening, an electronic medical record (EMR) reminder was created for our primary care practice. Screening rates before and after implementation were assessed to determine the impact of the reminder on screening rates. METHODS: A retrospective cohort analysis was performed for patients age 18-65 with visits between January 1, 2012-October 30, 2014. EMR databases were examined for HIV testing and selected patient characteristics. We evaluated the probability of HIV screening in unscreened patients before and after the reminder and used a multivariable generalized linear model to test the association between likelihood of HIV testing and specific patient characteristics. RESULTS: Prior to the reminder, the probability of receiving an HIV test for previously unscreened patients was 15.3%. This increased to 30.7% after the reminder (RR 2.02, CI 1.95-2.09, p < 0.0001). The impact was most significant in patients age 45-65. White race, English as primary language, and higher median household income were associated with lower likelihoods of screening both before and after implementation (RR 0.68, CI 0.65-0.72; RR 0.74, CI 0.67-0.82; RR 0.84, CI 0.80-0.88, respectively). CONCLUSIONS: The EMR reminder increased rates of HIV screening twofold in our practice. It was most effective in increasing screening rates in older patients. Patients who were white, English-speaking, and had higher incomes were less likely to be screened for HIV both before and after the reminder.

Assessment of Intensive Care Unit Laboratory Values That Differ From Reference Ranges and Association With Patient Mortality and Length of Stay.

Importance: Laboratory data are frequently collected throughout the care of critically ill patients. Currently, these data are interpreted by comparison with values from healthy outpatient volunteers. Whether this is the most useful comparison has yet to be demonstrated. Objectives: To understand how the distribution of intensive care unit (ICU) laboratory values differs from the reference range, and how these distributions are related to patient outcomes. Design, Setting, and Participants: Cross-sectional study of a large critical care database, the Medical Information Mart for Intensive Care database, from January 1, 2001, to October 31, 2012. The database is collected from ICU data from a large tertiary medical center in Boston, Massachusetts. The data are collected from medical, cardiac, neurologic, and surgical ICUs. All patients in the database from all ICUs for 2001 to 2012 were included. Common laboratory measurements over the time window of interest were sampled. The analysis was conducted from March to June 2017. Main Outcomes and Measures: The overlapping coefficient and Cohen standardized mean difference between distributions were calculated, and kernel density estimate visualizations for the association between laboratory values and the probability of death or quartile of ICU length of stay were created. Results: Among 38 605 patients in the ICU (21 852 [56.6%] male; mean [SD] age, 74.5 [55.1] years), 8878 (23%) had the best outcome (ICU survival, shortest quartile length of stay) and 3090 (8%) had the worst outcome (ICU nonsurvival). Distribution curves based on ICU data differed significantly from the hospital standard range (mean [SD] overlapping coefficient, 0.51 [0.32-0.69]). All laboratory values for the best outcome group differed significantly from those in the worst outcome group. Both the best and worst outcome group curves revealed little overlap with and marked divergence from the reference range. Conclusions and Relevance: The standard reference ranges obtained from healthy volunteers differ from the analogous range generated from data from patients in intensive care. Laboratory data interpretation may benefit from greater consideration of clinically contextual and outcomes-related factors.

Price of High-Throughput 25-Hydroxyvitamin D Immunoassays: Frequency of Inaccurate Results.

BACKGROUND: With a 10-year sustained increase in 25-hydroxyvitamin D [25(OH)D] testing, laboratories have swapped their LC-MS/MS methods for high-throughput automated immunoassays. Although it is generally well-known that immunoassays have poor recoveries for 25-hydroxyvitamin D2 [25(OH)D2], the frequency and extent to which this impacts total 25(OH)D have not been previously demonstrated. We evaluated 3 automated immunoassays against the first FDA-cleared CDC/NIST-traceable LC-MS/MS method. METHODS: Method comparison was performed for the Siemens ADVIA Centaur, Roche Elecsys Cobas, and Abbott Architect 25(OH)D immunoassay methods in real patient samples (n = 105). We calculated the mean bias in samples containing >20 ng/mL 25(OH)D2 and estimated the percent 25(OH)D2 cross-reactivities. We determined the prevalence of appreciable concentrations of 25(OH)D2 in our patient population through random sampling (n = 120) and projected the frequency of inaccurate 25(OH)D immunoassay results. RESULTS: Linear regression for 25(OH)D was y = 1.09x - 4.44 (Centaur), y = 0.84 + 0.43 (Cobas), and y = 0.83x - 0.48 (Architect). The mean biases of 25(OH)D concentrations were 5.6 (11.0) ng/mL (Centaur), -17.5 (7.2) ng/mL (Cobas), and -20.3 (9.8) ng/mL (Architect) in samples containing >20 ng/mL 25(OH)D2. The observed percent cross-reactivities for 25(OH)D2 were 115% (Centaur), 52% (Cobas), and 44% (Architect). We estimate that 8% of our population has >20 ng/mL 25(OH)D2, thereby compromising the accuracy of 25(OH)D results in >3000 samples annually. CONCLUSIONS: We demonstrate that immunoassay manufacturer package inserts indicate much better recoveries of 25(OH)D2 than what is observed in unadulterated real patient samples. We estimate the frequency of inaccurate total 25(OH)D determination by these immunoassay methods to be largely dependent on the concentration of 25(OH)D2 in each sample.