FDA's proposed rule for the regulation of laboratory-developed tests.

In October 2023, the Food and Drug Administration (FDA) released a proposed rule that ends enforcement discretion for laboratory-developed tests (LDTs). The FDA's proposal outlines a five-stage implementation to begin regulating LDTs as they do for commercial in vitro diagnostics (IVDs), including modified FDA-approved/cleared tests. We outline here concerns from the clinical and public health microbiology laboratory perspective. It is our opinion that LDTs performed by individual Clinical Laboratory Improvement Amendments-certified diagnostic laboratories should not be regulated in the same way as commercial IVDs. This rule, if finalized, will negatively impact the diagnostic services currently offered by clinical and public health laboratories and, therefore, patients and the providers who care for them. Ending enforcement discretion will likely stifle diagnostic innovation and decrease access to diagnostic testing and health equity. Furthermore, the lack of infrastructure, including personnel and funding, at the FDA and diagnostic laboratories to support the required submissions for review is an obstacle. Like the FDA, diagnostic laboratories prioritize patient safety, accurate clinical diagnostics, and health equity. Since the scope of the LDT landscape is currently unknown, we are supportive of a registration process, along with non-burdensome adverse event reporting, to first understand the scope of clinical use of LDTs and any associated safety concerns. Any regulatory rule should be based on data that have been gathered systematically, not anecdotes or case reports. A rule must also balance the potential negative impact to patient care with realistic safety risks for infectious disease diagnostics.

Direct-from-Blood Detection of Pathogens: a Review of Technology and Challenges.

Blood cultures have been the staple of clinical microbiology laboratories for well over half a century, but gaps remain in our ability to identify the causative agent in patients presenting with signs and symptoms of sepsis. Molecular technologies have revolutionized the clinical microbiology laboratory in many areas but have yet to present a viable alternative to blood cultures. There has been a recent surge of interest in utilizing novel approaches to address this challenge. In this minireview, I discuss whether molecular tools will finally give us the answers we need and the practical challenges of incorporating them into the diagnostic algorithm.

Role of diagnostic stewardship in reducing healthcare-facility-onset Clostridioides difficile infections.

We describe the implementation of an electronic medical record "hard stop" to decrease inappropriate Clostridioides difficile testing across a 5-hospital health system, effectively reducing the rates of healthcare-facility-onset C. difficile infection. This novel approach included expert consultation with medical director of infection prevention and control for test-order override.

The long-term sustainability of a respiratory culture nudge.

Resource-intensive interventions and education are susceptible to a lack of long-term sustainability and regression to the mean. The respiratory culture nudge changed reporting to "Commensal Respiratory Flora only: No S. aureus/MRSA or P. aeruginosa." This study demonstrated sustained reduction in broad-spectrum antibiotic duration and long-term sustainability 3 years after implementation.

Vaginal Swabs Are Non-inferior to Endocervical Swabs for Sexually Transmitted Infection testing in the Emergency Department.

STUDY OBJECTIVE: Emergency department (ED) testing for sexually transmitted infections (STI) in women is typically performed with a pelvic examination and an endocervical swab. However, vaginal swabs are effective for STI testing and the preferred specimen type according to the US Centers for Disease Control and Prevention. The utility of using vaginal swabs in the ED for STI screening has not been thoroughly investigated. Our objective was to assess detection rates for two bacterial STIs before and after implementing a screening protocol using vaginal swabs. METHODS: We conducted a quasi-experimental, pre-post study using standardized data from electronic health records across nine metropolitan Detroit hospital EDs. Patients included women who were tested for Chlamydia trachomatis or Neisseria gonorrhoeae in the ED between April 2018-December 2019. Pre-implementation tests from April 2018-February 2019 were done using endo-cervical swabs, and post-implementation tests from February 2019-December 2019 were done with vaginal swabs. We used non-inferiority testing for proportion with a non-inferiority margin of one percentage point absolute difference in detection rates of STI. RESULTS: The study included 22,291 encounters with 11,732 in the pre-implementation and 10,559 in the post-implementation phases. The C. trachomatis detection rates were 7.5% pre-implementation and 7.6% post-implementation (between-group difference, 0.1 percentage points; 95% confidence interval [CI]: -0.7, 0.4; p<.01 for non-inferiority). The N. gonorrhoeae detection rates were 3.1% pre-implementation and 3.6% post-implementation (between-group difference, 0.5 percentage points; 95% CI: -0.8, 0.04; p<.01 for non-inferiority). CONCLUSION: Using vaginal swabs for STI testing in the ED may be a non-inferior alternative to using endocervical swabs.

Performance of the Reveal Rapid Antibiotic Susceptibility Testing System on Gram-Negative Blood Cultures at a Large Urban Hospital.

Timely and effective antibiotic treatment is vital for sepsis, with increasing incidence of antimicrobial-resistant bacteremia driving interest in rapid phenotypic susceptibility testing. To enable the widespread adoption needed to make an impact, antibiotic susceptibility testing (AST) systems need to be accurate, enable rapid intervention, have a broad antimicrobial menu and be easy to use and affordable. We evaluated the Specific Reveal (Specific Diagnostics, San Jose, CA) rapid AST system on positive blood cultures with Gram-negative organisms in a relatively resistant population in a large urban hospital to assess its potential for routine clinical use. One hundred four randomly selected positive blood cultures (Virtuo; bioMérieux) were Gram stained, diluted 1:1,000 in Pluronic water, inoculated into 96-well antibiotic plates, sealed with the Reveal sensor panel, and placed in the Reveal instrument for incubation and reading. The MIC and susceptible/intermediate/resistant category was determined and compared to results from Vitek 2 (bioMérieux) for the 17 antimicrobials available and to Sensititre (Thermo Fisher) for 24 antimicrobials. Performance was also assessed with contrived blood cultures with 33 highly resistant strains. Reveal was in 98.0% essential agreement (EA) and 96.3% categorical agreement (CA) with Sensititre, with just 1.3% very major error (VME) and 97.0%/96.2%/1.3% EA/CA/VME versus Vitek 2. Reveal results for contrived highly resistant strains were equivalent, with EA/CA/VME of 97.7%/95.2%/1.0% with CDC/FDA Antibiotic Resistance Isolate Bank references. Average time to result (TTR) for Reveal was 4.6 h. Sample preparation was relatively low skill and averaged 3 min. We conclude that the Reveal system enables accurate and rapid susceptibility testing of Gram-negative blood cultures.

Risk Factors Associated With Hospitalization and Death in COVID-19 Breakthrough Infections.

Background: Characterizations of coronavirus disease 2019 (COVID-19) vaccine breakthrough infections are limited. We aim to characterize breakthrough infections and identify risk factors associated with outcomes. Methods: This was a retrospective case series of consecutive fully vaccinated patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a multicenter academic center in Southeast Michigan, between December 30, 2020, and September 15, 2021. Results: A total of 982 patients were identified; the mean age was 57.9 years, 565 (59%) were female, 774 (79%) were White, and 255 (26%) were health care workers (HCWs). The median number of comorbidities was 2; 225 (23%) were immunocompromised. BNT162b2 was administered to 737 (75%) individuals. The mean time to SARS-CoV-2 detection was 135 days. The majority were asymptomatic or exhibited mild to moderate disease, 154 (16%) required hospitalization, 127 (13%) had severe-critical illness, and 19 (2%) died. Age (odds ratio [OR], 1.14; 95% CI, 1.04-1.07; P < .001), cardiovascular disease (OR, 3.02; 95% CI, 1.55-5.89; P = .001), and immunocompromised status (OR, 2.57; 95% CI, 1.70-3.90; P < .001) were independent risk factors for hospitalization. Additionally, age (OR, 1.06; 95% CI, 1.02-1.11; P = .006) was significantly associated with mortality. HCWs (OR, 0.15; 95% CI, 0.05-0.50; P = .002) were less likely to be hospitalized, and prior receipt of BNT162b2 was associated with lower odds of hospitalization (OR, 0.436; 95% CI, 0.303-0.626; P < .001) and/or death (OR, 0.360; 95% CI, 0.145-0.898; P = .029). Conclusions: COVID-19 vaccines remain effective at attenuating disease severity. However, patients with breakthrough infections necessitating hospitalization may benefit from early treatment modalities and COVID-19-mitigating strategies, especially in areas with substantial or high transmission rates.

Hepatitis C Virus Reflex Testing Protocol in an Emergency Department.

INTRODUCTION: Our aim was to measure hepatitis C virus (HCV) screening and linkage-to-care rates in an urban emergency department (ED) before and after implementing an HCV viral RNA (vRNA) reflex testing protocol within a HCV screening program for at-risk patients. Our hypothesis was that using a reflex testing protocol would increase HCV testing rates of at-risk patients in the ED, which would increase the linkage-to-care rate. METHODS: In August 2018, our institution implemented an automated, electronic health record-based HCV screening protocol in the ED for at-risk patients. In January 2019, we implemented an HCV vRNA reflex testing protocol (reflex testing) for all positive HCV antibody (Ab) tests that were initiated through the screening protocol. We compared completion rates of HCV vRNA testing and the rate of linkage to care for patients with positive HCV Ab test results before and after implementation of reflex testing (five months per study period). RESULTS: Prior to reflex testing implementation, 233/425 (55%) patients with a positive HCV Ab test had an HCV vRNA test performed, whereas 270/323 (84%) patients with a positive HCV Ab test result had vRNA testing after reflex testing implementation (odds ratio [OR], 4.2; 95% confidence interval (CI): 3.0-6.0; P < 0.001). Of the eligible patients with positive HCV Ab test results who could be linked to care, 45 (10.6%) were linked to care before HCV reflex implementation and 46 (14.2%) were linked to care with reflex testing (OR, 1.4; 95% CI: 0.9-2.2; P = 0.13). CONCLUSION: Implementing a reflex testing initiative into an HCV screening program in the ED can result in an increase of the percentage of patients who receive an HCV vRNA test after having had a positive HCV Ab. Hepatitis C virus vRNA reflex testing was not associated with a statistically significant increase in linkage-to-care rates for HCV Ab-positive patients; however, further studies are required.

Evaluation of the selection of cerebrospinal fluid testing in suspected meningitis and encephalitis.

Diagnostic stewardship interventions can decrease unnecessary antimicrobial therapy and microbiology laboratory resources and costs. This retrospective cross-sectional study evaluated factors associated with inappropriate initial cerebrospinal fluid (CSF) testing in patients with suspected community-acquired meningitis or encephalitis. In 250 patients, 202 (80.8%) and 48 (19.2%) were suspected meningitis and encephalitis, respectively. 207 (82.8%) patients had inappropriate and 43 (17.2%) appropriate testing. Any inappropriate CSF test was greatest in the immunocompromised (IC) group (n = 54, 91.5%), followed by non-IC (n = 109, 80.1%) and HIV (n = 44, 80%). Ordering performed on the general ward was associated with inappropriate CSF test orders (adjOR 2.81, 95% CI [1.08-7.34]). Laboratory fee costs associated with excessive testing was close to $300,000 per year. A stepwise algorithm defining empiric and add on tests according to CSF parameters and patient characteristics could improve CSF test ordering in patients with suspected meningitis or encephalitis.

SARS-CoV-2 RT-PCR positivity and antibody prevalence among asymptomatic hospital-based health care workers.

BACKGROUND: The level of asymptomatic infection with SARS-CoV-2 could be substantial and among health care workers (HCWs) a source of continuing transmission of the virus to patients and co-workers. OBJECTIVES: Measure the period prevalence of SARS-CoV-2 PCR positivity and seroprevalence of SARS-CoV-2 IgG antibodies among a random sample of asymptomatic health system hospital-based health care workers (HCWs) 6½ -15½ weeks after 4/5/2020, the peak of the first surge of COVID-19 admissions. RESULTS: Of 524 eligible and consented participants from four metropolitan hospitals, nasopharyngeal swabs were obtained from 439 (83.8 %) and blood from 374 (71.4 %). Using PCR nucleic acid-based amplification (NAAT) methods, the period prevalence of SARS-CoV-2 infection was 0.23 % (95 % confidence interval (CI) 0.01 %-1.28 %; 1/439) from 5/21/20-7/16/20. The seroprevalence of SARS-CoV-2 IgG antibodies from June 17-July 24, 2020 was 2.41 % (95 % CI 1.27 %-4.51 %; 9/374). Those who were reactive were younger (median age 36 versus 44 years; p = 0.050), and those with self-reported Hispanic/Latino ethnicity had a higher seroprevalence (2/12 = 16.7 % versus 7/352 = 2.0 %; p = 0.051). There were no significant differences by sex, race, residence, hospital, unit or job type. The one employee who was found to be PCR test positive in this study was also reactive for IgG antibodies, tested 27 days later. CONCLUSIONS: The period prevalence of PCR positivity to SARS-CoV-2 and IgG seroprevalence was unexpectedly low in asymptomatic HCWs after a peak in COVID-19 admissions and the establishment of state and institutional infection control policies, suggesting that routine screening tests while community prevalence is relatively low would produce a minimal yield.

The Need for Dedicated Microbiology Leadership in the Clinical Microbiology Laboratory.

Clinical microbiology laboratories play a crucial role in patient care using traditional and innovative diagnostics. Challenges faced by laboratories include emerging pathogens, rapidly evolving technologies, health care-acquired infections, antibiotic-resistant organisms, and diverse patient populations. Despite these challenges, many clinical microbiology laboratories in the United States are not directed by doctoral level microbiology-trained individuals with sufficient time dedicated to laboratory leadership. The manuscript highlights the need for medical microbiology laboratory directors with appropriate training and qualifications.

Point-of-Care Testing in Microbiology.

Point-of-care (POC) or near patient testing for infectious diseases is a rapidly expanding space that is part of an ongoing effort to bring care closer to the patient. Traditional POC tests were known for their limited utility, but advances in technology have seen significant improvements in performance of these assays. The increasing promise of these tests is also coupled with their increasing complexity, which requires the oversight of qualified laboratory-trained personnel.

Multicenter Evaluation of a PCR-Based Digital Microfluidics and Electrochemical Detection System for the Rapid Identification of 15 Fungal Pathogens Directly from Positive Blood Cultures.

Routine identification of fungal pathogens from positive blood cultures by culture-based methods can be time-consuming, delaying treatment with appropriate antifungal agents. The GenMark Dx ePlex investigational use only blood culture identification fungal pathogen panel (BCID-FP) rapidly detects 15 fungal targets simultaneously in blood culture samples positive for fungi by Gram staining. We aimed to determine the performance of the BCID-FP in a multicenter clinical study. Blood culture samples collected at 10 United States sites and tested with BCID-FP at 4 sites were compared to the standard-of-care microbiological and biochemical techniques, fluorescence in situ hybridization using peptide nucleic acid probes (PNA-FISH) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Discrepant results were analyzed by bi-directional PCR/sequencing of residual blood culture samples. A total of 866 clinical samples, 120 retrospectively and 21 prospectively collected, along with 725 contrived samples were evaluated. Sensitivity and specificity of detection of Candida species (C. albicans, C. auris, C. dubliniensis, C. famata, C. glabrata, C. guilliermondii, C. kefyr, C. krusei, C. lusitaniae, C. parapsilosis, and C. tropicalis) ranged from 97.1 to 100% and 99.8 to 100%, respectively. For the other organism targets, sensitivity and specificity were as follows: 100% each for Cryptococcus neoformans and C. gattii, 98.6% and 100% for Fusarium spp., and 96.2% and 99.9% for Rhodotorula spp., respectively. In 4 of the 141 clinical samples, the BCID-FP panel correctly identified an additional Candida species, undetected by standard-of-care methods. The BCID-FP panel offers a faster turnaround time for identification of fungal pathogens in positive blood cultures that may allow for earlier antifungal interventions and includes C. auris, a highly multidrug-resistant fungus.

Clinical Performance of the Novel GenMark Dx ePlex Blood Culture ID Gram-Positive Panel.

Rapid identification from positive blood cultures is standard of care (SOC) in many clinical microbiology laboratories. The GenMark Dx ePlex Blood Culture Identification Gram-Positive (BCID-GP) Panel is a multiplex nucleic acid amplification assay based on competitive DNA hybridization and electrochemical detection using eSensor technology. This multicenter study compared the investigational-use-only (IUO) BCID-GP Panel to other methods of identification of 20 Gram-positive bacteria, four antimicrobial resistance genes, and both Pan Candida and Pan Gram-Negative targets that are unique to the BCID-GP Panel. Ten microbiology laboratories throughout the United States collected residual, deidentified positive blood culture samples for analysis. Five laboratories tested both clinical and contrived samples with the BCID-GP Panel. Comparator identification methods included each laboratory's SOC, which included matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and automated identification systems as well as targeted PCR/analytically validated real-time PCR (qPCR) with bidirectional sequencing. A total of 2,342 evaluable samples (1,777 clinical and 565 contrived) were tested with the BCID-GP Panel. The overall sample accuracy for on-panel organisms was 89% before resolution of discordant results. For pathogenic Gram-positive targets (Bacillus cereus group, Enterococcus spp., Enterococcus faecalis, Enterococcus faecium, Staphylococcus spp., Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lugdunensis, Listeria spp., Listeria monocytogenes, Streptococcus spp., Streptococcus agalactiae, Streptococcus anginosus group, Streptococcus pneumoniae, and Streptococcus pyogenes), positive percent agreement (PPA) and negative percent agreement (NPA) ranged from 93.1% to 100% and 98.8% to 100%, respectively. For contamination rule-out targets (Bacillus subtilis group, Corynebacterium, Cutibacterium acnes, Lactobacillus, and Micrococcus), PPA and NPA ranged from 84.5% to 100% and 99.9% to 100%, respectively. Positive percent agreement and NPA for the Pan Candida and Pan Gram-Negative targets were 92.4% and 95.7% for the former and 99.9% and 99.6% for the latter. The PPAs for resistance markers were as follows: mecA, 97.2%; mecC, 100%; vanA, 96.8%; and vanB, 100%. Negative percent agreement ranged from 96.6% to 100%. In conclusion, the ePlex BCID-GP Panel compares favorably to SOC and targeted molecular methods for the identification of 20 Gram-positive pathogens and four antimicrobial resistance genes in positive blood culture bottles. This panel detects a broad range of pathogens and mixed infections with yeast and Gram-negative organisms from the same positive blood culture bottle.

Direct Detection of Pathogens in Bloodstream During Sepsis: Are We There Yet?

BACKGROUND: Advances in medicine have improved our understanding of sepsis, but it remains a major cause of morbidity and mortality. The detection of pathogens that cause sepsis remains a challenge for clinical microbiology laboratories. CONTENT: Routine blood cultures are time-consuming and are negative in a large proportion of cases, leading to excessive use of broad-spectrum antimicrobials. Molecular testing direct from patient blood without the need for incubation has the potential to fill the gaps in our diagnostic armament and complement blood cultures to provide results in a timely manner. Currently available platforms show promise but have yet to definitively address gaps in sensitivity and specificity. SUMMARY: Significant strides have been made in the detection of pathogens directly from blood. A number of hurdles, however, remain before this technology can be adapted for routine use.

Improving care for critically ill patients with community-acquired pneumonia.

PURPOSE: The purpose of this study was to improve antimicrobial management and outcomes of critically ill patients with community-acquired pneumonia (CAP) through implementation of a pharmacist-driven bundle for ordering evidence-based diagnostic tests in a medical intensive care unit (MICU). METHODS: An inpatient collaborative practice agreement (CPA) was established for MICU pharmacists to order criteria-driven diagnostic testing for CAP from November 2017-March 2018. Adults admitted to the MICU and started on empiric antibiotics for CAP were included. The intervention arm was compared with a standard of care (SOC) group from November 2016-March 2017. RESULTS: Ninety-one patients were included in each group. There was no difference in the median antibiotic duration between SOC and CPA, at 7 days (interquartile range [IQR], 6-10) versus 7 days (IQR, 6-8), respectively. The overall use of evidence-based diagnostic tests increased in the CPA group. Patients in the CPA group had more frequent pathogen identification (SOC and CPA, respectively: 31 [34%] versus 46 [51%], p = 0.035) and antimicrobial deescalation (24 [26%] versus 53 [58%], p < 0.001). There was no significant difference in length of intensive care unit stay, at 4 days for SOC (IQR, 2-10) versus 6 days for CPA (IQR, 3-10), and no significant difference in inpatient all-cause mortality (13 [14%] versus 7 [8%]), retreatment 14 [15%] versus 11 [12%]), or 30-day readmission 16 ([18%] versus 13 [14%]) for SOC and CPA, respectively. The CPA was the only variable that was independently associated with antimicrobial deescalation (odds ratio, 4.030; 95% confidence interval, 2.101-7.731) in a multiple logistic regression. CONCLUSION: Implementation of a pharmacy-driven pneumonia diagnostic stewardship bundle improved the use of evidence-based diagnostics and increased the frequency of pathogen identification. This intervention was associated with increased antimicrobial deescalation without a negative impact on patient safety outcomes.

T2 Candida versus beta-D-glucan to facilitate antifungal discontinuation in the intensive care unit.

T2 Magnetic Resonance Candida Panel (T2MR) detects Candida directly in blood. Rapid turnaround time and high negative predictive value make it a useful diagnostic test to support antifungal discontinuation. This retrospective quasi-experiment compared empiric anidulafungin days of therapy (DOTs) in intensive care unit (ICU) patients with suspected candidemia that had negative blood cultures and negative 1,3-ß-D-glucan (BDG) versus negative blood cultures and negative T2MR. In 206 ICU patients, median anidulafungin DOTs were 2 (1, 5) compared to 1 (1, 2), respectively (P < 0.001); T2MR was associated with early discontinuation, AdjOR 3.0 95% CI (1.7-5.6), P < 0.001. Proven candidemia after discontinuation of anidulafungin occurred in 3% of BDG and 2% of T2MR patients at a median of 8 and 21 days, respectively. T2MR testing supports safe, early discontinuation of empiric antifungal therapy in ICU patients with suspected candidemia. Prospective studies to better define the role of T2MR in antifungal stewardship are warranted.