At-home testing for respiratory viruses: a minireview of the current landscape.

The landscape of at-home testing using over-the-counter (OTC) tests has been evolving over the last decade. The United States Food and Drug Administration Emergency Use Authorization rule has been in effect since the early 2000s, and it was widely employed during the severe acute respiratory syndrome coronavirus 2 pandemic to authorize antigen and nucleic acid detection tests for use in central laboratories as well as OTC. During the pandemic, the first at-home tests for respiratory viruses became available for consumer use, which opened the door for additional respiratory virus OTC tests. Concerns may exist regarding the public's ability to properly collect samples, perform testing, interpret results, and report results to public health authorities. However, favorable comparison studies between OTC testing and centralized laboratory test results suggest that OTC testing may have a place in healthcare, and it is likely here to stay. This mini-review of OTC tests for viral respiratory diseases will briefly cover the regulatory and reimbursement environment, current OTC test availability, as well as the advantages and limitations of OTC tests.

Validation of a Novel, Rapid Sepsis Diagnostic for Emergency Department Use.

OBJECTIVES: To assess the in vitro IntelliSep test, a microfluidic assay that quantifies the state of immune activation by evaluating the biophysical properties of leukocytes, as a rapid diagnostic for sepsis. DESIGN: Prospective cohort study. SETTING: Five emergency departments (EDs) in Louisiana, Missouri, North Carolina, and Washington. PATIENTS: Adult patients presenting to the ED with signs (two of four Systemic Inflammatory Response Syndrome criteria, where one must be temperature or WBC count) or suspicion (provider-ordered culture) of infection. INTERVENTIONS: All patients underwent testing with the IntelliSep using ethylene diamine tetraacetic acid-anticoagulated whole blood followed by retrospective adjudication for sepsis by sepsis-3 criteria by a blinded panel of physicians. MEASUREMENTS AND MAIN RESULTS: Of 599 patients enrolled, 572 patients were included in the final analysis. The result of the IntelliSep test is reported as the IntelliSep Index (ISI), ranging from 0.1 to 10.0, divided into three interpretation bands for the risk of sepsis: band 1 (low) to band 3 (high). The median turnaround time for ISI results was 7.2 minutes. The ISI resulted band 1 in 252 (44.1%), band 2 in 160 (28.0%), and band 3 in 160 (28.0%). Sepsis occurred in 26.6% (152 of 572 patients). Sepsis prevalence was 11.1% (95% CI, 7.5-15.7%) in band 1, 28.1% (95% CI, 21.3-35.8%) in band 2, and 49.4% (95% CI, 41.4-57.4%) in band 3. The Positive Percent Agreement of band 1 was 81.6% and the Negative Percent Agreement of band 3 was 80.7%, with an area under the receiver operating characteristic curve of 0.74. Compared with band 1, band 3 correlated with adverse clinical outcomes, including mortality, and resource utilization. CONCLUSIONS: Increasing ISI interpretation band is associated with increasing probability of sepsis in patients presenting to the ED with suspected infection.

Variability in Provider Assessment of Sepsis and Potential of Host Response Technology to Address this Dilemma-Results of an Online Delphi Study.

Potentially septic patients have a huge clinical and economic impact on hospitals and often present to the emergency department (ED) with undifferentiated symptoms. The triage of these patients is complex and has historically relied heavily upon provider judgment. This study aims to evaluate the consistency of provider judgment and the potential of a new host response sepsis test to aid in the triage process. A modified Delphi study involving 26 participants from multiple specialties was conducted to evaluate provider agreement about sepsis risk and to test proposed actions based on the results of a sepsis test. The participants considered case vignettes of potentially septic patients designed to represent diagnostic dilemmas. Provider assessment of sepsis risk in these cases ranged from 10% to 90% and agreement was poor. Agreement about clinical actions to take in response to testing improved when participants considered their own hypothetical borderline cases. New host response testing for sepsis may have the potential to improve sepsis diagnosis and care and should be applied in a protocolized fashion to ensure consistency of results.

Costs and Consequences of a Novel Emergency Department Sepsis Diagnostic Test: The IntelliSep Index.

Sepsis causes 270,000 deaths and costs $38 billion annually in the United States. Most cases of sepsis present in the emergency department (ED), where rapid diagnosis remains challenging. The IntelliSep Index (ISI) is a novel diagnostic test that analyzes characteristics of WBC structure and provides a reliable early signal for sepsis. This study performs a cost-consequence analysis of the ISI relative to procalcitonin for early sepsis diagnosis in the ED. PERSPECTIVE: U.S. healthcare system. SETTING: Community hospital ED. METHODS: A decision tree analysis was performed comparing ISI with procalcitonin. Model parameters included prevalence of sepsis, sensitivity and specificity of diagnostic tests (both ISI and procalcitonin), costs of hospitalization, and mortality rate stratified by diagnostic test result. Mortality and prevalence of sepsis were estimated from best available literature. Costs were estimated based on an analysis of a large, national discharge dataset, and adjusted to 2018 U.S. dollars. Outcomes included expected costs and survival. RESULTS: Assuming a confirmed sepsis prevalence of 16.9% (adjudicated to Sepsis-3), the ISI strategy had an expected cost per patient of $3,849 and expected survival rate of 95.08%, whereas the procalcitonin strategy had an expected cost of $4,656 per patient and an expected survival of 94.98%. ISI was both less costly and more effective than procalcitonin, primarily because of fewer false-negative results. These results were robust in sensitivity analyses. CONCLUSIONS: ISI was both less costly and more effective in preventing mortality than procalcitonin, primarily because of fewer false-negative results. The ISI may provide health systems with a higher-value diagnostic test in ED sepsis evaluation. Additional work is needed to validate these results in clinical practice.

Rapid identification of sepsis in the emergency department.

Objectives: Recent research has helped define the complex pathways in sepsis, affording new opportunities for advancing diagnostics tests. Given significant advances in the field, a group of academic investigators from emergency medicine, intensive care, pathology, and pharmacology assembled to develop consensus around key gaps and potential future use for emerging rapid host response diagnostics assays in the emergency department (ED) setting. Methods: A modified Delphi study was conducted that included 26 panelists (expert consensus panel) from multiple specialties. A smaller steering committee first defined a list of Delphi statements related to the need for and future potential use of a hypothetical sepsis diagnostic test in the ED. Likert scoring was used to assess panelists agreement or disagreement with statements. Two successive rounds of surveys were conducted and consensus for statements was operationally defined as achieving agreement or disagreement of 75% or greater. Results: Significant gaps were identified related to current tools for assessing risk of sepsis in the ED. Strong consensus indicated the need for a test providing an indication of the severity of dysregulated host immune response, which would be helpful even if it did not identify the specific pathogen. Although there was a relatively high degree of uncertainty regarding which patients would most benefit from the test, the panel agreed that an ideal host response sepsis test should aim to be integrated into ED triage and thus should produce results in less than 30 minutes. The panel also agreed that such a test would be most valuable for improving sepsis outcomes and reducing rates of unnecessary antibiotic use. Conclusion: The expert consensus panel expressed strong consensus regarding gaps in sepsis diagnostics in the ED and the potential for new rapid host response tests to help fill these gaps. These finding provide a baseline framework for assessing key attributes of evolving host response diagnostic tests for sepsis in the ED.

Surveillance cultures following a regional outbreak of carbapenem-resistant Acinetobacter baumannii.

OBJECTIVES: The primary aim of this study was to assess the epidemiology of carbapenem-resistant Acinetobacter baumannii (CRAB) for 9 months following a regional outbreak with this organism. We also aimed to determine the differential positivity rate from different body sites and characterize the longitudinal changes of surveillance test results among CRAB patients. DESIGN: Observational study. SETTING: A 607-bed tertiary-care teaching hospital in Milwaukee, Wisconsin. PATIENTS: Any patient admitted from postacute care facilities and any patient housed in the same inpatient unit as a positive CRAB patient. METHODS: Participants underwent CRAB surveillance cultures from tracheostomy secretions, skin, and stool from December 5, 2018, to September 6, 2019. Cultures were performed using a validated, qualitative culture method, and final bacterial identification was performed using mass spectrometry. RESULTS: In total, 682 patients were tested for CRAB, of whom 16 (2.3%) were positive. Of the 16 CRAB-positive patients, 14 (87.5%) were residents from postacute care facilities and 11 (68.8%) were African American. Among positive patients, the positivity rates by body site were 38% (6 of 16) for tracheal aspirations, 56% (9 of 16) for skin, and 82% (13 of 16) for stool. CONCLUSIONS: Residents from postacute care facilities were more frequently colonized by CRAB than patients admitted from home. Stool had the highest yield for identification of CRAB.

Rapid identification from rectal swabs of the clinically most relevant carbapenemase genes from gram-negative bacteria using the BD MAX Check-Points CPO Assay.

We conducted an international multicentre evaluation to assess the clinical performance characteristics of the new multiplex PCR-based BD MAX Check-Points CPO assay to detect the 5 major carbapenemase families: KPC, VIM/IMP (tested simultaneously), NDM and OXA-48 compared to a reference method consisting of 2 culture methods (to improve recovery of CPO isolates from the rectal swabs), followed by carbapenem susceptibility testing and sequencing of target carbapenemase genes. Tests were performed from rectal swab specimens in ESwab collection and transport devices. Positive percent agreement (PPA) for BD MAX Check-Points CPO for KPC and OXA-48 were 88.2% (95% CI:72.6-96.7) and 96.2% (95% CI:80.4-99.9), respectively. Negative percent agreement was ≥99% for each gene. Insufficient samples (≤10) were positive for VIM/IMP or NDM tests to calculate meaningful PPA values. The BD MAX Check-Points CPO assay represents an accurate tool for rapid recognition of patients with rectal colonization by the most commonly encountered CPOs.

Cytotoxic CD8-positive T-lymphocyte infiltration in the lungs as a histological pattern of SARS-CoV-2 pneumonitis.

Despite millions of PCR confirmed cases of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection, the long-term pathophysiological changes induced by this infection in the lungs and their relationship with possible immune triggers remain incompletely understood. Acute respiratory distress syndrome and subsequent respiratory failure are the most common causes of mortality in hospitalised patients. Severe lung tissue destruction can be due to an overactive immune system that far exceeds the harm that would have been caused by direct virus replication. This study extends our previous investigation and presents detailed histopathological findings on cryotransbronchial biopsy in patients with persistent (range 31-182 days) pneumonitis and severe interstitial inflammatory infiltration in the lungs due to SARS-CoV-2 infection. We describe a novel lung injury pattern associated with SARS-CoV-2 pneumonitis, which manifests as a marked interstitial CD8-positive T-cell lymphocytic infiltration. These findings provide a better understanding of the changes in the lungs that ensue due to SARS-CoV-2 infection.

Comparison of Methods for Determining the Antibiotic Susceptibility of Aerococcus Species in a Clinical Setting.

OBJECTIVES: Aerococcus spp are Gram-positive cocci increasingly recognized as uropathogens. The Clinical and Laboratory Standards Institute recently published specific breakpoints for Aerococcus spp (M45, third edition); however, the standardized method used for antimicrobial susceptibility testing (AST) requires media not often maintained in clinical laboratories. The purpose of this study was to evaluate and compare alternative methods of AST for Aerococcus isolates. METHODS: AST was performed on 134 clinical isolates using the Etest on three different types of agar, Vitek 2, and BD Phoenix. These results were compared with broth microdilution using the Sensititre STP6F. RESULTS: Aerococcus exhibited low minimum inhibitory concentrations to benzylpenicillin, meropenem, linezolid, and vancomycin. Variable resistance was seen to levofloxacin, ceftriaxone, and tetracycline. Meropenem and vancomycin met all acceptance criteria with every alternative method tested. Benzylpenicillin and linezolid did not meet essential agreement on any AST method. Tetracycline met the majority of acceptance criteria with the exception of more than 3% very major error when using the Etest on chocolate agar, the Vitek 2, and BD Phoenix. CONCLUSIONS: Overall, the alternate AST method with the highest agreement with broth microdilution was the Etest on Mueller-Hinton agar with 5% sheep blood and may be an optimal alternative to broth microdilution.

Point-of-care COVID-19 testing in the emergency department: current status and future prospects.

INTRODUCTION: This expert review outlines current and future point-of-care technologies for the diagnosis of the SARS-CoV-2 virus, which is responsible for causing coronavirus disease COVID-19 in the emergency department. COVID-19 first emerged in late 2019 and is responsible for a range of presentations from minor upper respiratory tract symptoms to severe pneumonia and multisystem organ failure. Among the technologies available include the gold standard of molecular point-of-care tests as well as antigen detection tests. AREAS COVERED: We discuss point-of-care molecular tests including multiplex, targeted, and single plex panels as well as various antigen testing methodologies in terms of availability and performance characteristics. In addition, we focus on current testing best practices and considerations for point-of-care testing in the emergency department based on a search of the literature available in PubMed to date and a review of FDA and CDC guidance. EXPERT OPINION: While there have been many advances in SARS-CoV-2 point-of-care testing, there remain challenges to implementation in the emergency department setting. A paradigm shift is needed to improve diagnosis and clinical outcomes.

Evaluation of a High-Definition PCR Assay for the Detection of SARS-CoV-2 in Extracted and Nonextracted Respiratory Specimens Collected in Various Transport Media.

OBJECTIVES: We conducted an analytic and clinical comparison of a novel high-definition polymerase chain reaction PCR (HDPCR) assay to traditional real-time PCR (RT-PCR) for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper respiratory specimens. METHODS: Analytic performance of RT-PCR, HDPCR, and extraction-free HDPCR was established through replicate testing of a serially diluted clinical specimen containing SARS-CoV-2. A clinical comparison of all 3 assays was conducted using 351 prospectively collected upper respiratory swab specimens obtained from symptomatic and asymptomatic individuals collected in various transport media. RESULTS: RT-PCR and HDPCR assays using extracted nucleic acid demonstrated similar analytic limits of detection (LoD) and clinical performance, with 100% positive and negative agreement. Extraction-free HDPCR demonstrated a 1.5 to 2.0 log10 increase in LoD based on cycle threshold values. However, clinical performance of extraction-free HDPCR remained high, demonstrating 97.8% positive and 99.6% negative agreement with RT-PCR. An overall increase in "invalid" and "presumptive" results was observed when using the extraction-free method, but this was highly variable based on transport medium used. CONCLUSIONS: HDPCR performs similar to RT-PCR for the detection of SARS-CoV-2. The use of an extraction-free HDPCR protocol maintained high clinical performance despite reduced analytic LoD, with the benefit of reduced hands-on time and cost of reagents associated with nucleic acid extraction.

Can a Clean Catch Urine Sample Be Used to Diagnose Chlamydia and Gonorrhea in Adolescent Females?

PURPOSE: Clean catch urine samples may be an alternative specimen to test for chlamydia and gonorrhea infections. The aim of this study was to determine the sensitivity and specificity of clean urine for chlamydia and gonorrhea in women. METHODS: This was a noninferiority prospective cohort study of women aged 14-22 years requiring chlamydia and gonorrhea testing. Patients provided a vaginal swab (gold standard), clean urine (test sample), and dirty urine (usual care). All samples were analyzed using Hologic's Aptima Combo2 Assay, a second-generation nucleic acid amplification test. The sensitivity and specificity of the clean and dirty urine were calculated and compared. RESULTS: Three hundred and twenty-three females were included, mean age 17.0 ± 1.6 years. For chlamydia, 59 participants were positive by vaginal swab. The sensitivity of clean urine to diagnose chlamydia was 86.2% (95% CI: 74.8%-93.1%) and specificity was 98.8% (95% CI: 96.5%-99.8%). The sensitivity of dirty urine to diagnose chlamydia was 89.8% (95% CI: 79.2%-95.6%), and the specificity was 99.6% (95% CI 97.6%-100%). For gonorrhea, 18 participants were positive by vaginal swab. The sensitivity of clean urine to diagnose gonorrhea was 94.4% (95% CI: 72.4%-100%) and specificity was 99.7% (95% CI: 98.0%-100.0%). The sensitivity of dirty urine to diagnose gonorrhea was 100% (95% CI: 79.3%-100%) and specificity was 99.7% (95% CI: 98.0%-100%). Specificity of clean urine was noninferior compared with dirty urine for diagnosing chlamydia (p = .0004) and gonorrhea (p < .0001). CONCLUSIONS: Clean urine samples may be an alternative option to diagnose chlamydia and gonorrhea in women.

Toxigenic Clostridioides difficile colonization as a risk factor for development of C. difficile infection in solid-organ transplant patients.

BACKGROUND: The association between Clostridioides difficile colonization and C. difficile infection (CDI) is unknown in solid-organ transplant (SOT) patients. We examined C. difficile colonization and healthcare-associated exposures as risk factors for development of CDI in SOT patients. METHODS: The retrospective study cohort included all consecutive SOT patients with at least 1 screening test between May 2017 and April 2018. CDI was defined as the presence of diarrhea (without laxatives), a positive C. difficile clinical test, and the use of C. difficile-directed antimicrobial therapy as ordered by managing clinicians. In addition to demographic variables, exposures to antimicrobials, immunosuppressants, and gastric acid suppressants were evaluated from the time of first screening test to the time of CDI, death, or final discharge. RESULTS: Of the 348 SOT patients included in our study, 33 (9.5%) were colonized with toxigenic C. difficile. In total, 11 patients (3.2%) developed CDI. Only C. difficile colonization (odds ratio [OR], 13.52; 95% CI, 3.46-52.83; P = .0002), age (OR, 1.09; CI, 1.02-1.17; P = .0135), and hospital days (OR, 1.05; 95% CI, 1.02-1.08; P = .0017) were independently associated with CDI. CONCLUSIONS: Although CDI was more frequent in C. difficile colonized SOT patients, the overall incidence of CDI was low in this cohort.

Impact of an Antimicrobial Stewardship Program Pharmacist During Microbiology Rounds.

OBJECTIVES: The purpose of this study is to describe and evaluate the impact of the participation of an antimicrobial stewardship program (ASP) pharmacist in microbiology rounds at our institution. METHODS: This single-center retrospective descriptive study included inpatient and ambulatory adults (≥18 years) with a susceptibility request reviewed during microbiology rounds between October 2018 and March 2019. In October 2018, multidisciplinary telephone microbiology rounds were initiated with the medical directors of the clinical microbiology laboratory and ASP pharmacist to review susceptibility requests. Numbers and types of interventions made by an ASP pharmacist and potential benefits were recorded and analyzed. RESULTS: Sixty-seven susceptibility requests were reviewed by an ASP pharmacist, of which 83.6% were inpatient. An ASP pharmacist completed chart reviews for 92.5% of requests and contacted the requester or primary team 74.6% of the time. About half (47.8%) of susceptibility requests were approved, and only 65.2% of requests from an infectious diseases provider were approved (P = .039). The most frequent potential benefits of the intervention included preventing unnecessary susceptibility testing (47.8%), improving clinician understanding (40.3%), and preventing treatment of a culture result deemed as a contaminant (19.4%). CONCLUSIONS: ASP pharmacists are uniquely accessible and able to assist with preventing unnecessary susceptibility testing, optimizing antimicrobial therapy, and providing education to other health care professionals.

SARS-CoV-2 Cycle Thresholds, Poverty, Race, and Clinical Outcomes.

BACKGROUND: Poverty and high viral load are associated with worse outcomes among COVID-19 patients. METHODS: We included patients admitted to Froedtert Health between March 16 and June 1, 2020. SARS-CoV-2 viral load was proxied by cycle-threshold values. To measure poverty, we used Medicaid or uninsured status and residence in socially disadvantaged areas. We assessed the association between viral load and length of stay and discharge disposition, while controlling for demographics and confounders. RESULTS: Higher viral load was associated with longer length of stay (coefficient -0.02; 95% CI, -0.04 to 0.01; P = 0.006) and higher likelihood of death (coefficient -0.11; 95% CI, -0.17 to -0.06; P < 0.001). Poverty, residence in disadvantaged areas, and race were not. DISCUSSION: This study confirms a relationship of viral load with in-hospital death, even after controlling for race and poverty.

A Multi-mRNA Host-Response Molecular Blood Test for the Diagnosis and Prognosis of Acute Infections and Sepsis: Proceedings from a Clinical Advisory Panel.

Current diagnostics are insufficient for diagnosis and prognosis of acute infections and sepsis. Clinical decisions including prescription and timing of antibiotics, ordering of additional diagnostics and level-of-care decisions rely on understanding etiology and implications of a clinical presentation. Host mRNA signatures can differentiate infectious from noninfectious etiologies, bacterial from viral infections, and predict 30-day mortality. The 29-host-mRNA blood-based InSepTM test (Inflammatix, Burlingame, CA, formerly known as HostDxTM Sepsis) combines machine learning algorithms with a rapid point-of-care platform with less than 30 min turnaround time to enable rapid diagnosis of acute infections and sepsis, as well as prediction of disease severity. A scientific advisory panel including emergency medicine, infectious disease, intensive care and clinical pathology physicians discussed technical and clinical requirements in preparation of successful introduction of InSep into the market. Topics included intended use; patient populations of greatest need; patient journey and sample flow in the emergency department (ED) and beyond; clinical and biomarker-based decision algorithms; performance characteristics for clinical utility; assay and instrument requirements; and result readouts. The panel identified clear demand for a solution like InSep, requirements regarding test performance and interpretability, and a need for focused medical education due to the innovative but complex nature of the result readout. Innovative diagnostic solutions such as the InSep test could improve management of patients with suspected acute infections and sepsis in the ED, thereby lessening the overall burden of these conditions on patients and the healthcare system.

Racial Disparities in Incidence and Outcomes Among Patients With COVID-19.

Importance: Initial public health data show that Black race may be a risk factor for worse outcomes of coronavirus disease 2019 (COVID-19). Objective: To characterize the association of race with incidence and outcomes of COVID-19, while controlling for age, sex, socioeconomic status, and comorbidities. Design, Setting, and Participants: This cross-sectional study included 2595 consecutive adults tested for COVID-19 from March 12 to March 31, 2020, at Froedtert Health and Medical College of Wisconsin (Milwaukee), the largest academic system in Wisconsin, with 879 inpatient beds (of which 128 are intensive care unit beds). Exposures: Race (Black vs White, Native Hawaiian or Pacific Islander, Native American or Alaska Native, Asian, or unknown). Main Outcomes and Measures: Main outcomes included COVID-19 positivity, hospitalization, intensive care unit admission, mechanical ventilation, and death. Additional independent variables measured and tested included socioeconomic status, sex, and comorbidities. Reverse transcription polymerase chain reaction assay was used to test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Results: A total of 2595 patients were included. The mean (SD) age was 53.8 (17.5) years, 978 (37.7%) were men, and 785 (30.2%) were African American patients. Of the 369 patients (14.2%) who tested positive for COVID-19, 170 (46.1%) were men, 148 (40.1%) were aged 60 years or older, and 218 (59.1%) were African American individuals. Positive tests were associated with Black race (odds ratio [OR], 5.37; 95% CI, 3.94-7.29; P = .001), male sex (OR, 1.55; 95% CI, 1.21-2.00; P = .001), and age 60 years or older (OR, 2.04; 95% CI, 1.53-2.73; P = .001). Zip code of residence explained 79% of the overall variance in COVID-19 positivity in the cohort (ρ = 0.79; 95% CI, 0.58-0.91). Adjusting for zip code of residence, Black race (OR, 1.85; 95% CI, 1.00-3.65; P = .04) and poverty (OR, 3.84; 95% CI, 1.20-12.30; P = .02) were associated with hospitalization. Poverty (OR, 3.58; 95% CI, 1.08-11.80; P = .04) but not Black race (OR, 1.52; 95% CI, 0.75-3.07; P = .24) was associated with intensive care unit admission. Overall, 20 (17.2%) deaths associated with COVID-19 were reported. Shortness of breath at presentation (OR, 10.67; 95% CI, 1.52-25.54; P = .02), higher body mass index (OR per unit of body mass index, 1.19; 95% CI, 1.05-1.35; P = .006), and age 60 years or older (OR, 22.79; 95% CI, 3.38-53.81; P = .001) were associated with an increased likelihood of death. Conclusions and Relevance: In this cross-sectional study of adults tested for COVID-19 in a large midwestern academic health system, COVID-19 positivity was associated with Black race. Among patients with COVID-19, both race and poverty were associated with higher risk of hospitalization, but only poverty was associated with higher risk of intensive care unit admission. These findings can be helpful in targeting mitigation strategies for racial disparities in the incidence and outcomes of COVID-19.

Distribution of SARS-CoV-2 PCR Cycle Threshold Values Provide Practical Insight Into Overall and Target-Specific Sensitivity Among Symptomatic Patients.

OBJECTIVES: We examined the distribution of reverse transcription polymerase chain reaction (RT-PCR) cycle threshold (CT) values obtained from symptomatic patients being evaluated for coronavirus disease 2019 (COVID-19) to determine the proportion of specimens containing a viral load near the assay limit of detection (LoD) to gain practical insight to the risk of false-negative results. We also examined the relationship between CT value and patient age to determine any age-dependent difference in viral load or test sensitivity. METHODS: We collected CT values obtained from the cobas severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) assay corresponding to 1,213 combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals that were reported as positive or presumptive positive for SARS-CoV-2. CT values were stratified by SARS-CoV target and patient age group. RESULTS: In total, 93.3% to 98.4% of specimens demonstrated CT values greater than 3× the assay LoD, at which point false-negative results would not be expected. The mean of CT values between age groups was statistically equivalent with the exception of patients in age group 80 to 89 years, which demonstrated slightly lower CTs. CONCLUSIONS: Based on the distribution of observed CT values, including the small proportion of specimens with values near the assay LoD, there is a low risk of false-negative RT-PCR results in combined nasopharyngeal-oropharyngeal specimens obtained from symptomatic individuals.

Achromobacter xylosoxidans Cellular Pathology Is Correlated with Activation of a Type III Secretion System.

Achromobacter xylosoxidans is increasingly recognized as a colonizer of cystic fibrosis (CF) patients, but the role that A. xylosoxidans plays in pathology remains unknown. This knowledge gap is largely due to the lack of model systems available to study the toxic potential of this bacterium. Recently, a phospholipase A2 (PLA2) encoded by a majority of A. xylosoxidans genomes, termed AxoU, was identified. Here, we show that AxoU is a type III secretion system (T3SS) substrate that induces cytotoxicity to mammalian cells. A tissue culture model was developed showing that a subset of A. xylosoxidans isolates from CF patients induce cytotoxicity in macrophages, suggestive of a pathogenic or inflammatory role in the CF lung. In a toxic strain, cytotoxicity is correlated with transcriptional activation of axoU and T3SS genes, demonstrating that this model can be used as a tool to identify and track expression of virulence determinants produced by this poorly understood bacterium.