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.

Development and validation of a standardized blood culture contamination definition and metric dashboard for a large health care system.

OBJECTIVES: Blood culture contamination is a major problem in health care, with significant impacts on both patient safety and cost. Initiatives to reduce blood culture contamination require a reliable, consistent metric to track the success of interventions. The objective of our project was to establish a standardized definition of blood culture contamination suitable for use in a Veterans Health Administration (VHA) national data query, then to validate this definition and query. A secondary objective was to construct a national VHA data dashboard to display the data from this query that could be used in VHA quality improvement projects aimed at reducing blood culture contamination. METHODS: A VHA microbiology expert work group was formed to generate a standardized definition and oversee the validation studies. The standardized definition was used to generate data for calendar year 2021 using a Structured Query Language data query. Twelve VHA hospital microbiology laboratories compared the data from the query against their own locally derived contamination data and recorded those data in a data collection worksheet that all sites used. Data were collated and presented to the work group. RESULTS: More than 50,000 blood culture accessions were in the validation data set, with more than 1,200 contamination events. The overall blood culture contamination rate for the 12 facilities participating was 2.56% with local definitions and data and 2.43% with the standardized definitions and data query. The main differences noted between the 2 data sets were deemed to be issues in local definitions. The query and definition were then converted into a national data dashboard that all VHA facilities can now access. CONCLUSIONS: A standardized definition for blood culture contamination and a national data query were validated for enterprise-wide VHA use. To our knowledge, this represents the first reported standardized, validated, and automated approach for calculating and tracking blood culture contamination. This tool will be key in quality initiatives aimed at reducing contamination events in VHA.

PROSER: A Web-Based Peripheral Blood Smear Interpretation Support Tool Utilizing Electronic Health Record Data.

OBJECTIVES: Peripheral blood smear (PBS) interpretation represents a cornerstone of pathology practice and resident training but has remained largely static for decades. Here, we describe a novel PBS interpretation support tool. METHODS: In a mixed-methods quality improvement study, a web-based clinical decision support (CDS) tool to assist pathologists in PBS interpretation, PROSER, was deployed in an academic hospital over a 2-month period in 2022. PROSER interfaced with the hospital system's electronic health record and data warehouse to obtain and display relevant demographic, laboratory, and medication information for patients with pending PBS consults. PROSER used these data along with morphologic findings entered by the pathologist to draft a PBS interpretation using rule-based logic. We evaluated users' perceptions of PROSER with a Likert-type survey. RESULTS: PROSER displayed 46 laboratory values with corresponding reference ranges and abnormal flags, allowed for entry of 14 microscopy findings, and computed 2 calculations based on laboratory values; it composed automated PBS reports using a library of 92 prewritten phrases. Overall, PROSER was well received by residents. CONCLUSIONS: In this quality improvement study, we successfully deployed a web-based CDS tool for PBS interpretation. Future work is needed to quantitatively evaluate this intervention's effects on clinical outcomes and resident training.

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.

Brief Report: Rates of Fentanyl Use Among Psychiatric Emergency Room Patients.

BACKGROUND AND OBJECTIVES: Opioid overdose-related deaths increased from approximately 18 000 deaths in 2007 to 46 802 deaths in 2018. Fentanyl is primarily responsible for the increase in opioid overdose deaths from 2011 through 2017. The primary aim of this study is to determine the rates of fentanyl in the urine drug screens of all patients who presented to the psychiatric emergency room at VA Connecticut, over 7 months in 2018. METHODS: Data were collected for all patient presentations between June 2018 and December 2018. There were 746 total patient presentations, with 497 being unique. Collected data included basic demographic information, psychiatric diagnosis, and urine drug screen for various illicit substances, including fentanyl. RESULTS: Over 15% of patients screened positive for fentanyl. Patients who tested positive for fentanyl were further classified based on positive urine drug screening results for other opioids, cocaine, or both. Twenty percent of patients who screened positive for fentanyl and cocaine tested negative for other opioids. This category suggests that some veterans might be consuming fentanyl with cocaine. DISCUSSION AND CONCLUSIONS: Fentanyl was found at a high rate, even in the absence of other opioids, which suggests that some veterans might be consuming fentanyl with cocaine. Consequently, harm reduction strategies should be broadened to include all patients at risk of fentanyl overdose, including patients who use substances (eg, cocaine) that are potentially adulterated with fentanyl. SCIENTIFIC SIGNIFICANCE: This study is the first one of its kind that looked at rates of fentanyl use in all presentations to a psychiatric emergency room. While it is well-known that fentanyl is highly prevalent, these findings extend the current state of knowledge by replication in a psychiatric emergency population. (Am J Addict 2021;30:92-95).

Advances in rapid diagnostics for bloodstream infections.

Septicemia from bloodstream infections (BSI) is the second largest cause of inpatient mortality and the single most expensive condition for US hospitals to manage. There has been an explosive development of commercial diagnostic systems to accelerate the identification and antimicrobial susceptibility testing (AST) of causative pathogens. Despite adoption of advanced technologies like matrix-assisted laser desorption imaging-time-of-flight mass spectrometry and multiplex polymerase chain reaction for rapid identification, clinical impact has been variable, in part due to the persistent need for conventional AST as well as prescriber understanding of these rapidly evolving platforms. Newer technologies are expanding on rapid detection of genotypic determinants of resistance, but only recently has rapid phenotypic AST been available. Yet, improved outcomes with rapid diagnostic platforms are still most evident in conjunction with active antimicrobial stewardship. This review will outline key advancements in rapid diagnostics for BSI and the role of antimicrobial stewardship in this new era.

The Development and Implementation of a Novel Electronic Consult System by a Laboratory Medicine Service: Experience From the First 2 Years of Use.

CONTEXT.­: A novel electronic consult (e-consult) system for a pathology and laboratory medicine service (PLMS) was implemented in 2015 at a high-complexity Veterans Administration health care facility. Consults were previously made through direct provider communication without documentation in the medical record. OBJECTIVE.­: To evaluate the utilization trends of the laboratory e-consult system at the Department of Veterans Affairs Connecticut facility during the first 2 years since inception. DESIGN.­: E-consultation involves pathology and laboratory medicine resident review followed by attending pathologist review and cosignature. E-consults to the pathology and laboratory medicine service from 2015 to 2017 were reviewed to record type of consult, requesting department, patient location, and turnaround time. RESULTS.­: The pathology and laboratory medicine service received 351 e-consults from 2015 to 2017. The volume varied by subsection: hematology and coagulation (215 of 351; 61%), chemistry (109 of 351; 31%), blood bank (19 of 351; 6%), and microbiology/virology (8 of 351; 2%). Hematology and coagulation consults were entirely for peripheral blood smear review (215 of 215; 100%). Chemistry consults were placed for toxicology/drugs of abuse (81 of 109; 74%), test utilization (17 of 109; 16%), or nontoxicology (11 of 109; 10%). Three services placed the majority of consults: primary care (279 of 351; 80%), hematology/oncology (39 of 351; 11%), and psychiatry (27 of 351; 8%). The median turnaround time for completion of e-consults was 1.2 days. Since e-consult implementation, the mean number of consults increased from 8.6/mo in 2015 to 18.1/mo in 2017, peaking in the last quarter of analysis in 2017 with a mean of 25.3 consults/mo. CONCLUSIONS.­: This novel e-consult system improved accessibility to and documentation of answers to laboratory questions and increased the visibility of the pathology and laboratory medicine service. Future goals include development of outcomes-based measures to better assess the clinical impact of e-consults.

Do I Have HIV or Not? Lack of RNA Detection and the Case for Sensitive DNA Testing.

We present a case of a 20-year-old male who had ambiguous HIV test results after entering new provider care and whose status was later complicated by undetectable viral RNA off antiretroviral therapy (ART). Verifying HIV infection status may occasionally require sensitive DNA testing that might need to be considered in diagnostic guidelines to resolve diagnosis and ensure appropriate ART management.

Application, Verification, and Implementation of SARS-CoV-2 Serologic Assays with Emergency Use Authorization.

Interest continues to grow regarding the role of serologic assays for the detection of prior infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The U.S. Food and Drug Administration (FDA) has granted emergency use authorization (EUA) status to many SARS-CoV-2 serologic assays. In this document, expert recommendations from clinical microbiologist members of the American Society for Microbiology (ASM) concerning detailed verification strategies for SARS-CoV-2 serologic assays with FDA EUA are provided, as are insights into assay limitations and reporting considerations for laboratories. Assessments concerning single-antibody and multiantibody isotype detection assays, which may provide either differentiated or nondifferentiated (i.e., total antibody) antibody class results, are addressed. Additional considerations prior to assay implementation are also discussed, including biosafety, quality control, and proficiency testing strategies. As the landscape of SARS-CoV-2 serologic testing is rapidly changing, this document provides updated guidance for laboratorians on application of these assays.

When Should Asymptomatic Persons Be Tested for COVID-19?

On 24 August 2020, the Centers for Disease Control and Prevention (CDC) updated its website to highlight that asymptomatic individuals, even those with exposure to a COVID-19-positive contact, do not necessarily need to be tested unless they have medical conditions associated with increased risk of severe illness from COVID-19. The CDC subsequently updated its guidance on 19 September 2020 to support testing of asymptomatic persons, including close contacts of persons with documented SARS-CoV-2 infection. In this editorial, the American Society for Microbiology Clinical and Public Health Microbiology Committee's Subcommittee on Laboratory Practices comments on testing of asymptomatic individuals relative to current medical knowledge of the virus and mitigation measures. Specific points are provided concerning such testing when undertaking contact tracing and routine surveillance. Limitations to consider when testing asymptomatic persons are covered, including the need to prioritize testing of contacts of positive COVID-19 cases. We urge the CDC to consult with primary stakeholders of COVID-19 testing when making such impactful changes in testing guidance.

SARS-CoV-2 detection in setting of viral swabs scarcity: Are MRSA swabs and viral swabs equivalent?

BACKGROUND: The global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown. METHODS: We compared simultaneous nasal MRSA swabs (COPAN ESwabs ® 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress ® SARS-CoV-2 assay. RESULTS: Of the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs ® 480C and the viral swabs in 78 (96.3%). CONCLUSION: We found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19.

Case Report: Disseminated Strongyloidiasis in a Patient with COVID-19.

The SARS-CoV-2 virus has emerged and rapidly evolved into a current global pandemic. Although bacterial and fungal coinfections have been associated with COVID-19, little is known about parasitic infection. We report a case of a COVID-19 patient who developed disseminated strongyloidiasis following treatment with high-dose corticosteroids and tocilizumab. Screening for Strongyloides infection should be pursued in individuals with COVID-19 who originate from endemic regions before initiating immunosuppressive therapy.

Stethoscope hygiene: Using cultures and real-time feedback with bioluminescence-based adenosine triphosphate technology to change behavior.

BACKGROUND: Stethoscope hygiene is rarely done despite guideline recommendations. We wanted to determine whether demonstrating what is growing on the stethoscopes of providers via culture or bioluminescence technology alters perceptions and improves compliance. METHODS: Providers were given the opportunity to (1) culture their stethoscopes before and after disinfection with alcohol pads, alcohol-based hand rub, or hydrogen peroxide disinfectant wipes and (2) swab stethoscopes for bioluminescence-based adenosine triphosphate testing before and after disinfection. Outcomes were observed for hand and stethoscope hygiene rates and before and after intervention survey responses. The bacteria that were isolated, colony-forming units (CFU), and bioluminescence scores were tracked. RESULTS: A total of 1,245 observed hand hygiene opportunities showed that compliance improved from 72.5%-82.3% (P < .001). In addition, 590 observed patient-provider encounters revealed no significant change in stethoscope hygiene rates of 10% initially and 5% afterward (P = .08), although self-reported rates trended from 56%- 67% postintervention (P = .06). Perceptions regarding stethoscope hygiene importance improved (8.5/10 to 9.3/10; P = .04). Disinfection with alcohol pads, alcohol-based hand rub, and hydrogen peroxide disinfectant wipes were equivalent in CFU reduction (P = .21). CONCLUSIONS: Showing providers what is growing on their stethoscopes via cultures and bioluminescence technology before and after disinfection improved "buy in" regarding stethoscope hygiene importance. Both methods were rated as having an equal impact, however, objective observations failed to show improvement.

Distributed Microbiology Testing: Bringing Infectious Disease Diagnostics to Point of Care.

We discuss the current practice of point-of-care diagnostics in infectious diseases as methods transition from antigen-based to molecular, and beyond simple molecular to the next generations of point-of-care testing methods. We evaluate the role of point-of-care at different sites of care and describe and evaluate trends likely to be driven by advances in molecular methodology, emerging biomarkers, and informatics. We describe strengths, weaknesses, opportunities, and threats to the development of point-of-care diagnostics in the near (1-10 years) and more distant (10-20 years) future.

Ethics for Laboratory Medicine.

BACKGROUND: Laboratory medicine, like other areas of medicine, is obliged to adhere to high ethical standards. There are particular ethical issues that are unique to laboratory medicine and other areas in which ethical issues uniquely impact laboratory practice. Despite this, there is variability in ethics education within the profession. This review provides a foundation for the study of ethics within laboratory medicine. CONTENT: The Belmont Report identifies 3 core principles in biomedical ethics: respect for persons (including autonomy), beneficence (and its corollary nonmalfeasance), and justice. These core principles must be adhered to in laboratory medicine. Informed consent is vital to maintain patient autonomy. However, balancing patient autonomy with the desire for beneficence can sometimes be difficult when patients refuse testing or treatment. The use of leftover or banked samples is fundamental to the ability to do research, create reference intervals, and develop new tests, but it creates problems with consent. Advances in genetic testing have created unique ethical issues regarding privacy, incidental findings, and informed consent. As in other professions, the emergence of highly contagious and deadly infectious diseases poses a difficult ethical dilemma of helping patients while protecting healthcare workers. CONCLUSIONS: Although many clinical laboratorians do not see or treat patients, they must be held accountable to the highest ethical and professional behavior. Recognition and understanding of ethical issues are essential to ethical practice of laboratory medicine.

Fermi-LAT Observations of γ-Ray Emission toward the Outer Halo of M31.

The Andromeda galaxy is the closest spiral galaxy to us and has been the subject of numerous studies. It harbors a massive dark matter halo, which may span up to ~600 kpc across and comprises ~90% of the galaxy's total mass. This halo size translates into a large diameter of 42° on the sky, for an M31-Milky Way (MW) distance of 785 kpc, but its presumably low surface brightness makes it challenging to detect with γ-ray telescopes. Using 7.6 yr of Fermi Large Area Telescope (Fermi-LAT) observations, we make a detailed study of the γ-ray emission between 1-100 GeV toward M31's outer halo, with a total field radius of 60° centered at M31, and perform an in-depth analysis of the systematic uncertainties related to the observations. We use the cosmic-ray propagation code GALPROP to construct specialized interstellar emission models to characterize the foreground γ-ray emission from the MW, including a self-consistent determination of the isotropic component. We find evidence for an extended excess that appears to be distinct from the conventional MW foreground, having a total radial extension upward of ~120-200 kpc from the center of M31. We discuss plausible interpretations of the excess emission, but emphasize that uncertainties in the MW foreground-and in particular, modeling of the H i-related components-have not been fully explored and may impact the results.