Bard, Jennifer Dien

Abstract This publication represents the first part of an update to the clinical practice guideline on the diagnosis and management of group A streptococcal (GAS) pharyngitis, developed by the Infectious Diseases Society of America (IDSA). Diagnosis of GAS pharyngitis by clinician judgment alone is unreliable, and universal testing incurs cost and inconvenience for individuals at low risk of having GAS infection. Clinical scoring systems have been used to quantify the probability of a positive GAS throat culture based on standardized criteria such as the presence of fever, tonsillar enlargement or exudate, tender and enlarged anterior cervical lymph nodes, and the absence of cough. The goal of this manuscript is to review the evidence and provide a recommendation as to whether a scoring system should be used to decide which patients should have a GAS diagnostic test (ie, rapid antigen test [RADT], molecular method, and/or throat culture) performed. We performed a systematic review of randomized and nonrandomized studies that compared the use of a clinical scoring system to clinician judgment alone in predicting the result of a throat culture. Evidence from studies in children and adults suggests the diagnostic accuracy is comparable or slightly higher using a scoring system compared to clinician judgment alone. Although the studies are limited due to small size, lack of uniformity in outcome measures, and incomplete data, the consensus of the panel is that the balance of benefits and harms favors incorporation of a clinical scoring system as part of the evaluation of patients with sore throat and suspected GAS pharyngitis.

Abstract This publication represents the first part of an update to the clinical practice guideline on the diagnosis and management of group A streptococcal (Streptococcus pyogenes or GAS) pharyngitis, developed by the Infectious Diseases Society of America (IDSA). Diagnosis of GAS pharyngitis by clinician judgment alone is unreliable, and unselective testing incurs cost and inconvenience for individuals at low risk of having GAS infection. Clinical scoring systems have been used to quantify the probability of a positive GAS throat culture based on standardized criteria such as the presence of fever; tonsillar enlargement or exudate; tender and enlarged anterior cervical lymph nodes; and the absence of cough. The goal of this article is to determine whether a scoring system should be used to decide which patients should have a diagnostic test performed by rapid antigen detection test, molecular methods, and/or throat culture. We performed a systematic review of randomized and nonrandomized studies that compared the use of a clinical scoring system to clinician judgment alone in predicting the outcome of a throat culture. Evidence from studies in children and adults suggests the diagnostic accuracy of a clinical scoring system is comparable to or slightly higher than clinician judgment alone. However, the studies are limited due to small size, lack of uniformity in outcome measures, and incomplete data. The consensus of the panel is that the balance of benefits and harms favors use of a clinical scoring system as part of the evaluation of patients with sore throat. The principal utility of using a scoring system is to identify patients with low probability of GAS pharyngitis and to reduce unnecessary testing.

SUMMARY Bloodstream infections (BSIs) are a significant cause of mortality and morbidity. Rapid identification of pathogens and detection of a few resistance markers from positive blood cultures are now possible through the increased availability of commercial rapid diagnostic tests, including nucleic acid amplification tests and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. This document describes the clinical utility of rapid diagnostics performed on positive blood cultures and provides evidence-based laboratory medicine guidelines for using rapid tests to diagnose BSIs in hospitalized adult and pediatric patients. This guideline was developed for use by medical (a.k.a. clinical) microbiologists, medical laboratory professionals, infectious disease clinicians, pharmacists, hospital administrators, healthcare providers, and other stakeholders associated with BSIs. A panel of experts, including medical microbiologists and experts in systematic literature review, was assembled to formulate the Population–Intervention–Comparison–Outcome (PICO) question, review the literature, and provide recommendations for using rapid tests to diagnose BSI and improve patient outcomes. A comprehensive literature search of four electronic bibliographic databases (MEDLINE, Embase, CINAHL, and Cochrane) was conducted to identify studies with measurable outcomes. The panel followed a systematic process, which included a standardized methodology for rating the certainty of the evidence and strength of recommendations using the GRADE (Grading of Recommendations, Assessment, Development, and Evaluation) approach. The panel evaluated the literature to answer the question: Does using rapid diagnostic tests improve clinical outcomes in adult and pediatric patients hospitalized with a BSI? Peer-reviewed literature was available to address three outcomes, including time to targeted therapy, mortality, and length of hospital stay. In general, the quality of the evidence was low to moderate due to the paucity of controlled, randomized clinical trial studies. However, eight recommendations were made based on evidence derived from the systematic review of the published literature. To answer the PICO question, the expert committee recommended using rapid diagnostic tests combined with active communication to decrease the time to targeted therapy and length of stay (strong recommendation). While the strength of the evidence for the impact on mortality is low, the panel supports using rapid tests to impact these outcomes. A summary of the recommendations is listed in the Executive Summary, which includes a detailed description of the background, methods, evidence summary, and rationale that supports each recommendation in the full text.

Abstract Background We assessed how laboratories use and handle reporting of results of rapid diagnostics performed on positive blood culture broths, with a focus on antimicrobial resistance (AMR) markers. Methods A survey assembled by the Antibacterial Resistance Leadership Group Diagnostics Committee was circulated from December 2020 to May 2021. The survey was sent to local hospitals, shared on the ClinMicroNet and Division C listservs, and included in a College of American Pathologists proficiency testing survey. Results Ninety-six laboratories of various sizes across the United States (95%) and outside of the United States (5%) participated. Of the laboratories that had at least 1 rapid diagnostic in place (94%), significant heterogeneity in methods used and reporting practices was found across community (52%) and academic (40%) laboratories serving hospitals of various sizes. Respondents had implemented 1 to 6 different panels/platforms for a total of 31 permutations. Methods of reporting rapid organism identification and AMR results varied from listing all targets as “detected”/“not detected” (16–22%) without interpretive guidance, to interpreting results (23–42%), or providing therapeutic guidance comments to patient-facing healthcare teams (3–17%). Conclusions Current approaches to reporting molecular AMR test results from positive blood culture vary significantly across clinical laboratories. Providing interpretative comments with therapeutic guidance alongside results reported may assist clinicians who are not well-versed in genetic mechanisms of AMR. However, this is currently not being done in all clinical laboratories. Standardized strategies for AMR gene result reporting are needed.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with more than 2 million genomes sequenced at the time of writing. The rise of more transmissible variants of concern that impact vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution.

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with >2 million genomes sequenced at this writing. The rise of more transmissible variants of concern that affect vaccine and therapeutic effectiveness has led to widespread interest in SARS-CoV-2 evolution. Clinicians are also eager to take advantage of the information provided by SARS-CoV-2 genotyping beyond surveillance purposes. Here, we review the potential role of SARS-CoV-2 genotyping in clinical care. The review covers clinical use cases for SARS-CoV-2 genotyping, methods of SARS-CoV-2 genotyping, assay validation and regulatory requirements, clinical reporting for laboratories, and emerging issues in clinical SARS-CoV-2 sequencing. While clinical uses of SARS-CoV-2 genotyping are currently limited, rapid technological change along with a growing ability to interpret variants in real time foretell a growing role for SARS-CoV-2 genotyping in clinical care as continuing data emerge on vaccine and therapeutic efficacy.

Abstract Urinary tract infections (UTIs) are among the most common bacterial infections in the United States and are a major driver of antibiotic use, both appropriate and inappropriate, across healthcare settings. Novel UTI diagnostics are a strategy that might enable better UTI treatment. Members of the Antibacterial Resistance Leadership Group Laboratory Center and the Infectious Diseases Society of America Diagnostics Committee convened to envision ideal future UTI diagnostics, with a view towards improving delivery of healthcare, patient outcomes and experiences, and antibiotic use, addressing which types of UTI diagnostics are needed and how companies might approach development of novel UTI diagnostics.