Clinically Adjudicated Reference Standards for Evaluation of Infectious Diseases Diagnostics

One Size Fits Small: The Narrow Utility for Plasma Metagenomics

Metagenomic sequencing of plasma has been advertised by Karius, Inc. as a way to diagnose a variety of infectious syndromes. Due to the lack of robust evidence of clinical utility, our laboratory began actively stewarding Karius testing. Microbiology Directors recommended cancelation of Karius orders when certain criteria were identified. We set out to review Karius test requests in a 52-month period of stewardship, during which we recommended cancellation on 21 of 57 orders (37%). Of Karius tests sent on samples with negative conventional testing, only 3 (7%) had positive results for Karius with plausible explanatory etiologies. Of these three cases, two were empirically covered for the positive finding without improvement and one case was never treated. Twelve (29%) had positive results that were noted by infectious diseases (ID) to reflect insignificant detections. Given the 4-fold higher detection of insignificant Karius results, we set out to systematically analyze the literature for the experience of insignificant detections at other centers. When we compared studies that included healthy controls or had clinical adjudication of positive Karius findings by ID physicians, we found a median of 17.5% of individual patients that had positive insignificant detections of potential pathogenic bacteria or fungi. The most frequently detected species were as likely to be clinically adjudicated to be insignificant as they were to be significant within the same studies. Overall, these findings highlight limited utility of Karius testing and a need for careful stewardship, not only to ensure it is sent on patients who may benefit, but also to ensure results of potential pathogens are interpreted cautiously.

Comparison of two rapid host-response tests for distinguishing bacterial and viral infection in adults with acute respiratory infection

OBJECTIVES

Distinguishing bacterial from viral acute respiratory infection (ARI) is challenging, leading to inappropriate antimicrobial use and antimicrobial resistance. We evaluated the accuracy of two host-response tests to differentiate bacterial and viral infection.

METHODS

This study used patient blood samples previously collected during a randomised controlled trial of adults hospitalised with ARI. The aetiology for each patient was clinically adjudicated. PAXgene blood RNA samples were tested using the TriVerity test (which measures 29 mRNAs) and serum samples were tested using the MeMed BV test (which measures 3 proteins). Diagnostic accuracy was calculated against adjudicated aetiology.

RESULTS

169 patients were tested. Median age was 60 (45-74) years and 152 (90%) received antibiotics. 60 (36%) were adjudicated as bacterial, 54 (32%) as viral, 26 (15%) as viral/bacterial co-infection, and 29 (17%) as non-infected. For bacterial (including bacterial/viral co-infection) versus non-bacterial infection, the TriVerity bacterial score had a Positive Percentage Agreement (PPA) of 81% (95%CI 70-89) and a Negative Percentage Agreement (NPA) of 66% (95%CI 55-79) and the MeMed BV score had a PPA of 96% (95%CI 90-99) and NPA of 34% (95%CI 23-47). The AUROC for the two tests was 0.77 (95%CI 0.70-0.84) and 0.81 (95%CI 0.74-0.87) respectively, p = 0.388.

CONCLUSIONS

Both tests demonstrated similar overall accuracy for distinguishing bacterial infection with the Triverity test missing some bacterial infections and MeMed BV misclassifying most viral infections as bacterial. Prospective impact studies evaluating antibiotic use, safety and cost effectiveness are now required.

A 29-mRNA host response test to identify bacterial and viral infections and to predict 30-day mortality in emergency department patients with suspected infections: A prospective observational cohort study

INTRODUCTION

The goal of this study is to validate the accuracy of the 29-mRNA host response classifiers Inflammatix Bacterial-Viral-Non infected-3b (IMX-BVN-3b) and Severity-3b (IMX-SEV-3b) to identify bacterial and viral infections and to predict 30-day mortality in patients with suspected infections in the ED.

METHODS

This prospective observational cohort study enrolled patients with suspected infections in a tertiary ED. IMX-BVN-3b was compared to clinically forced and consensus adjudicated bacterial/viral infection status and IMX-SEV-3b was compared to 30-day mortality.

RESULTS

A total of 688 patients were enrolled. Using forced adjudication, the AUC for the diagnosis of bacterial infection by IMX-BVN-3b was 0.76 (95 % CI: 0.72 - 0.80). The AUC for the diagnosis of viral infections was 0.89 (95 %CI 0.84-0.95). IMX-SEV-3b had an AUC of 0.77 (95 % CI: 0.68 - 0.85) on 30-day mortality.

CONCLUSION

The 29-gene host response classifiers IMX-BVN-3b and IMX-SEV-3b identify viral and bacterial infections and predict 30-day mortality in patients with suspected infections in the ED.

Daily Fungal Cell-Free DNA Testing to Assess Clinical Status during Candida krusei Fungemia

We present a case of a man immunocompromised due to myelodysplastic syndrome with Candida krusei fungemia who had a rising cell-free DNA (cfDNA) giant magnetoresistance (GMR) signal when tested daily using plasma blood samples. With the rise in GMR signal paralleling the development of skin lesions in this patient, we conclude that cfDNA can be used to indicate uncontrolled infection and thus help monitor response to therapy. This index patient provides evidence that an invasive fungal infection requires both direct antifungal therapy and an intact immune system to control the infection. This biosensing platform has been simplified to potentially serve as a point-of-care test, setting it apart by overcoming the three common barriers of cfDNA testing: complexity, cost, and time.

Real-life Assessment of BioFire FilmArray Pneumonia Panel in Adults Hospitalized With Respiratory Illness

BACKGROUND

Inability to identify the microbial etiology of lower respiratory tract infection leads to unnecessary antibiotic use. We evaluated the utility of the BioFire FilmArray Pneumonia Panel (BioFire PN) to inform microbiologic diagnosis.

METHODS

Hospitalized adults with respiratory illness were recruited; sputa and clinical/laboratory data were collected. Sputa were cultured for bacteria and tested with BioFire PN. Microbial etiology was adjudicated by 4 physicians. Bacterial polymerase chain reaction (PCR) was compared with culture and clinical adjudication.

RESULTS

Of 298 sputa tested, BioFire PN detected significantly more pathogens (350 bacteria, 16 atypicals, and 164 viruses) than sputum culture plus any standard-of-care testing (91% vs 60%, P < .0001). When compared with culture, the sensitivity of BioFire PN for individual bacteria was 46% to 100%; specificity, 61% to 100%; and negative predictive value, 92% to 100%. Cases were adjudicated as viral (n = 58) and bacterial (n = 100). PCR detected bacteria in 55% of viral cases and 95% of bacterial (P < .0001). High serum procalcitonin and bacterial adjudication were more often associated with sputa with 106 or 107 copies detected.

CONCLUSIONS

Multiplex PCR testing of sputa for bacteria is useful to rule out bacterial infection with added value to detect viruses and atypical bacteria.

Priorities and Progress in Diagnostic Research by the Antibacterial Resistance Leadership Group

The advancement of infectious disease diagnostics, along with studies devoted to infections caused by gram-negative and gram-positive bacteria, is a top scientific priority of the Antibacterial Resistance Leadership Group (ARLG). Diagnostic tests for infectious diseases are rapidly evolving and improving. However, the availability of rapid tests designed to determine antibacterial resistance or susceptibility directly in clinical specimens remains limited, especially for gram-negative organisms. Additionally, the clinical impact of many new tests, including an understanding of how best to use them to inform optimal antibiotic prescribing, remains to be defined. This review summarizes the recent work of the ARLG toward addressing these unmet needs in the diagnostics field and describes future directions for clinical research aimed at curbing the threat of antibiotic-resistant bacterial infections.

The Antibacterial Resistance Leadership Group: Scientific Advancements and Future Directions

In this overview, we describe important contributions from the Antibacterial Resistance Leadership Group (ARLG) to patient care, clinical trials design, and mentorship while outlining future priorities. The ARLG research agenda is focused on 3 key areas: gram-positive infections, gram-negative infections, and diagnostics. The ARLG has developed an innovative approach to clinical trials design, the desirability of outcome ranking (DOOR), which uses an ordinal measure of global outcome to assess both benefits and harms. DOOR was initially applied to observational studies to determine optimal dosing of vancomycin for methicillin-resistant Staphylcococcus aureus bacteremia and the efficacy of ceftazidime-avibactam versus colistin for the treatment of carbapenem-resistant Enterobacterales infection. DOOR is being successfully applied to the analysis of interventional trials and, in collaboration with the US Food and Drug Administration (FDA), for use in registrational trials. In the area of diagnostics, the ARLG developed Master Protocol for Evaluating Multiple Infection Diagnostics (MASTERMIND), an innovative design that allows simultaneous testing of multiple diagnostic platforms in a single study. This approach will be used to compare molecular assays for the identification of fluoroquinolone-resistant Neisseria gonorrhoeae (MASTER GC) and to compare rapid diagnostic tests for bloodstream infections. The ARLG has initiated a first-in-kind randomized, double-blind, placebo-controlled trial in participants with cystic fibrosis who are chronically colonized with Pseudomonas aeruginosa to assess the pharmacokinetics and antimicrobial activity of bacteriophage therapy. Finally, an engaged and highly trained workforce is critical for continued and future success against antimicrobial drug resistance. Thus, the ARLG has developed a robust mentoring program targeted to each stage of research training to attract and retain investigators in the field of antimicrobial resistance research.

Comparison of the AmpFire® Multiplex HPV Assay to the Xpert® HPV Assay for detection of human papillomavirus and cervical disease in women with human immunodeficiency virus: a pragmatic performance evaluation

BACKGROUND

Low- and middle-income countries (LMICs) account for nearly 85% of the global cervical cancer burden, yet have the least access to high-performance screening. International guidelines recommend human papillomavirus testing (HPV) as primary screening, yet implementation is inhibited by the cost of HPV testing. Atila AmpFire® HPV Assay (AmpFire) is both affordable and easy to use, and offers individual genotyping. The objective of this study was to compare the performance of the AmpFire HPV assay to the Xpert® HPV assay in detection of both HPV and clinically significant cervical disease.

METHODS

We utilized stored cervical specimens from a prospective cohort study of women living with human immunodeficiency virus (HIV) in Botswana conducted from May to July 2018. Positive and negative percent agreement was calculated for the AmpFire and Xpert assays, as was detection of high-grade cervical dysplasia.

RESULTS

63 stored cervical specimens had detectable DNA after thawing and were included in the analysis. The positive percent agreement was 91.2% (95%CI 76.3-98.1) and negative percent agreement was 79.3% (95% CI 60.3-92.0). Six cases positive by AmpFire but negative by Xpert were HPV genotypes 35, 52 (n = 2), 58, 68, and co-infection with HPV 45 and 68. Both Xpert and AmpFire assays detected HPV in all 10 samples of women who had high-grade cervical dysplasia.

CONCLUSIONS

The AmpFire HPV assay demonstrated excellent analytic performance in both detection of HPV and clinically significant cervical disease. AmpFire HPV is a promising option to increase access to affordable, type-specific HPV screening for cervical cancer in LMICs.