When less is more: the art of communicating clinical microbiology results.

The clinical microbiology laboratory is capable of identifying microorganisms in clinical specimens faster and more accurately than ever before. At face value, this should enable patient care providers to make better-informed decisions and target antimicrobial therapies to deliver individualized care. Ironically, more complete and specific reporting of microorganisms isolated from specimens may result in overtreatment based on the presence of a pathogen, even in the absence of clear signs of clinical infection.

Comparison of the Simplexa GBS Direct and ARIES GBS assays for the detection of in broth-enriched swab specimens.

We conducted a comparative evaluation of the FDA-cleared Simplexa GBS Direct and ARIES GBS molecular assays for the detection of (Group B , GBS) in 386 prospectively collected, broth-enriched vaginal/rectal swab specimens. The sensitivity of each test was 96.2% and specificity was ≥98.

Multiplex High-Definition Polymerase Chain Reaction Assay for the Diagnosis of Tick-borne Infections in Children.

Background: ticks can carry species as well as other pathogens that cause human disease. The frequency of tick-borne infections and coinfections in children with suspected Lyme disease is unknown, creating clinical uncertainty about the optimal approach to diagnosis.

Methods: We enrolled children aged 1-21 years presenting to 1 of 8 Pedi Lyme Net emergency departments for evaluation of Lyme disease.

A phase 2 trial of a topical antiseptic bundle in head and neck cancer surgery: Effects on surgical site infection and the oral microbiome.

Background: Head and neck cancer (HNC) surgery remains an important component of management but is associated with a high rate of surgical site infection (SSI). We aimed to assess the safety and efficacy of a topical mucosal antiseptic bundle in preventing SSI and evaluate microbial predictors of infection through a genomic sequencing approach.

Methods: This study was an open-label, single-arm, single-center, phase 2 trial of a topical mucosal antiseptic bundle in patients with HNC undergoing aerodigestive tract resection and reconstruction.

Commentary: Can Automated Blood Culture Systems Be Both New and Improved?

Automated continuous monitoring blood culture (CMBC) systems are a cornerstone of the clinical microbiology laboratory. Despite the critical role of these systems in diagnosing life-threatening bloodstream infections, their core technologies and performance characteristics have remained largely unchanged since their introduction in the 1990s. This stability and uniformity have enabled the development of quality benchmarks, such as percent positivity and contamination rate; downstream diagnostics, such as direct identification and susceptibility testing of microorganisms in positive cultures; and clinical guidelines based on time to positivity or duration of bacteriemia.

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.

Molecular Diagnosis of Pneumonia (Including Multiplex Panels).

Background: Pneumonia is a common illness, accounting for a staggering amount of worldwide morbidity and mortality. The diagnosis of pneumonia is challenging given the variety of responsible pathogens. Diagnostic testing for bacterial pneumonia has traditionally relied on time-consuming culture-based methods, though recently multiplexed molecular approaches have been described.

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.

A Multicenter Clinical Study To Demonstrate the Diagnostic Accuracy of the GenMark Dx ePlex Blood Culture Identification Gram-Negative Panel.

Bacteremia can progress to septic shock and death without appropriate medical intervention. Increasing evidence supports the role of molecular diagnostic panels in reducing the clinical impact of these infections through rapid identification of the infecting organism and associated antimicrobial resistance genes. We report the results of a multicenter clinical study assessing the performance of the GenMark Dx ePlex investigational-use-only blood culture identification Gram-negative panel (BCID-GN), a rapid diagnostic assay for detection of bloodstream pathogens in positive blood culture (PBC) bottles.

Severe Acute Respiratory Syndrome Coronavirus 2: The Emergence of Important Genetic Variants and Testing Options for Clinical Laboratories.

Monitoring the spread of emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants relies on rapid genetic testing of the viral genome. The sequencing method commonly called next-generation sequencing can identify virus variants. At times, for target-specific mutation detection, reverse transcriptase polymerase chain reaction is used to identify specific variants.

Surveillance cultures following a regional outbreak of carbapenem-resistant .

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.

"No distinction of Black or Fair": The Natural History of Race in Adam Ferguson's Lectures on Moral Philosophy.

Recent scholarship on the Scottish Enlightenment has emphasized the increasing importance, in the last decades of the eighteenth century, of the concept of race. Yet race was a conceptual, moral, and taxonomic puzzle for Scots intellectuals such as Adam Ferguson (1723-1816). While the influence of Ferguson's published works has received wide scholarly attention, the content of his teaching has not.

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.

Bronchoalveolar lavage-based COVID-19 testing in patients with cancer.

Objective/background: A few case reports in the setting of coronavirus disease 2019 (COVID-19) and multiplex polymerase chain reaction (PCR)-based assays for common respiratory pathogens have shown a higher yield of bronchoalveolar lavage (BAL) samples than upper airway specimens in immunocompromised patients.

Methods: A retrospective study was conducted reviewing patients diagnosed with COVID-19 at the Medical College of Wisconsin (Milwaukee, WI, USA) between March 13, 2020 and June 11, 2020. All patients tested positive for SARS-CoV-2 via real-time reverse transcriptase PCR (RT-PCR), through a nasopharyngeal or a bronchoscopy specimen.

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).

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.

Toxigenic colonization as a risk factor for development of 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.

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.

Direct detection of intact carbapenemase variants from cell lysates: Identification, characterization and clinical implications.

Introduction: Carbapenemase-producing organisms (CPOs) are a growing threat to human health. Among the enzymes conferring antibiotic resistance produced by these organisms, carbapenemase (KPC) is considered to be a growing global health threat. Reliable and specific detection of this antibiotic resistance-causing enzyme is critical both for effective therapy and to mitigate further spread.

Responding to the Challenges of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2): Perspectives from the Association for Molecular Pathology Infectious Disease Subdivision Leadership.

Clinical molecular laboratory professionals are at the frontline of the response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, providing accurate, high-quality laboratory results to aid in diagnosis, treatment, and epidemiology. In this role, we have encountered numerous regulatory, reimbursement, supply-chain, logistical, and systems challenges that we have struggled to overcome to fulfill our calling to provide patient care. In this Perspective from the Association for Molecular Pathology Infectious Disease Subdivision Leadership team, we review how our members have risen to these challenges, provide recommendations for managing the current pandemic, and outline the steps we can take as a community to better prepare for future pandemics.

Practical Comparison of the BioFire FilmArray Pneumonia Panel to Routine Diagnostic Methods and Potential Impact on Antimicrobial Stewardship in Adult Hospitalized Patients with Lower Respiratory Tract Infections.

Lower respiratory tract infections, including hospital-acquired and ventilator-associated pneumonia, are common in hospitalized patient populations. Standard methods frequently fail to identify the infectious etiology due to the polymicrobial nature of respiratory specimens and the necessity of ordering specific tests to identify viral agents. The potential severity of these infections combined with a failure to clearly identify the causative pathogen results in administration of empirical antibiotic agents based on clinical presentation and other risk factors.

Multicenter Evaluation of the BioFire FilmArray Pneumonia/Pneumonia Plus Panel for Detection and Quantification of Agents of Lower Respiratory Tract Infection.

The ability to provide timely identification of the causative agents of lower respiratory tract infections can promote better patient outcomes and support antimicrobial stewardship efforts. Current diagnostic testing options include culture, molecular testing, and antigen detection. These methods may require collection of various specimens, involve extensive sample treatment, and can suffer from low sensitivity and long turnaround times.

Evaluation of the WASPLab Segregation Software To Automatically Analyze Urine Cultures Using Routine Blood and MacConkey Agars.

Automation of the clinical microbiology laboratory has become more prominent as laboratories face higher specimen volumes and understaffing and are becoming more consolidated. One recent advancement is the use of digital image analysis to rapidly distinguish between chromogenic growth for screening bacterial cultures. In this study, colony segregation software developed by Copan (Brescia, Italy) was evaluated to distinguish between significant growth and no growth of urine cultures plated onto standard blood and MacConkey agars.

Association Between Environmental Factors and Toxigenic Clostridioides difficile Carriage at Hospital Admission.

Importance: Clostridioides difficile infection is the most frequent health care-associated infection in the United States. However, exposure to this organism might occur outside the health care setting.

Objective: To examine whether exposure to environmental factors, such as livestock farms, is associated with a higher probability of being colonized with C difficile at hospital admission.

How frequently should sink drains be disinfected?

Previously, we showed that disinfection of sink drains is effective at decreasing bacterial loads. Here, we report our evaluation of the ideal frequency of sink-drain disinfection and our comparison of 2 different hydrogen peroxide disinfectants.