Performance of two modified two-tier algorithms for the serologic diagnosis of Lyme disease.

We compared the performance of a new modified two-tier testing (MTTT) platform, the Diasorin Liaison chemiluminescent immunoassay (CLIA), to the Zeus enzyme-linked immunoassay (ELISA) MTTT and to Zeus ELISA/Viramed immunoblot standard two-tier testing (STTT) algorithm. Of 537 samples included in this study, 91 (16.9%) were positive or equivocal by one or more screening tests. Among these 91 samples, only 57 samples were concordant positive by first-tier screening tests, and only 19 of 57 were concordant by the three second-tier methods. For IgM results, positive percent agreement (PPA) was 68.1% for Diasorin versus 89.4% for Zeus compared to immunoblot. By contrast, the PPA for IgG for both Diasorin and Zeus was 100%. Using a 2-out-of-3 consensus reference standard, the PPAs for IgM were 75.6%, 97.8%, and 95.6% for Diasorin, Zeus, and immunoblot, respectively. The difference between Zeus MTTT and Diasorin MTTT for IgM detection was significant (P = 0.0094). PPA for both Diasorin and Zeus MTTT IgG assays was 100% but only 65.9% for immunoblot STTT (P = 0.0005). In total, second-tier positive IgM and/or IgG results were reported for 57 samples by Diasorin MTTT, 63 by Zeus MTTT, and 54 by Viramed STTT. While Diasorin CLIA MTTT had a much more rapid, automated, and efficient workflow, Diasorin MTTT was less sensitive for the detection of IgM than Zeus MTTT and STTT including in 5 early Lyme cases that were IgM negative but IgG positive. IMPORTANCE: The laboratory diagnosis of Lyme disease relies upon the detection of antibodies to Borrelia species. Standard two tier testing (STTT) methods rely upon immunoblots which have clinical and technical limitations. Modified two-tier testing (MTTT) methods have recently become available and are being widely adopted. There are limited independent data available assessing the performance of MTTT and STTT methods.

Atypical pneumonia testing in transplant recipients.

BACKGROUND: The incidence of atypical pneumonia among immunocompromised patients is not well characterized. Establishing a diagnosis of atypical pneumonia is challenging as positive tests must be carefully interpreted. We aimed to assess the test positivity rate and incidence of atypical pneumonia in transplant recipients. METHODS: A retrospective cohort study was conducted at the Yale New Haven Health System in Connecticut. Adults with solid organ transplant, hematopoietic stem cell transplant (HSCT), or chimeric antigen receptor T-cell, who underwent testing for atypical pathogens of pneumonia (Legionella pneumophilia, Mycoplasma pneumoniae, Chlamydia pneumoniae, and Bordetella pertussis) between January 2016 and August 2022 were included. Positive results were adjudicated in a clinical context using pre-defined criteria. A cost analysis of diagnostic testing was performed. RESULTS: Note that, 1021 unique tests for atypical pathogens of pneumonia were performed among 481 transplant recipients. The testing positivity rate was 0.7% (n = 7). After clinical adjudication, there were three cases of proven Legionella and one case of possible Mycoplasma infection. All cases of legionellosis were in transplant recipients within 1-year post-transplantation with recently augmented immunosuppression and lymphopenia. The possible case of Mycoplasma infection was in an HSCT recipient with augmented immunosuppression. The cost of all tests ordered was $50,797.73. CONCLUSION: The positivity rate of tests for atypical pneumonia was very low in this transplant cohort. An algorithmic approach that targets testing for those with compatible host, clinical, radiographic, and epidemiologic factors, and provides guidance on test selection and test interpretation, may improve the diagnostic yield and lead to substantial cost savings.

Proceedings of the Clinical Microbiology Open 2022-assessing clinical laboratory and industry responses to COVID-19 pandemic testing capacity challenges (part 1).

As the COVID-19 pandemic winds down, clinical and public health laboratories, along with industry partners, reflect on the successes and failures of the pandemic response. To capture the lessons learned and better prepare for the next pandemic, the Clinical Microbiology Open (CMO) assembled key stakeholders including directors of clinical laboratories, industry partners, and state and federal agencies such as the Centers for Disease Control and Prevention and the Food and Drug Administration. Participants were asked to provide their perspectives on the initial pandemic response, supply chain constraints especially during surges, staffing challenges, test triage and communication strategies, clinical informatics needs, laboratory financial impacts of SARS-CoV-2 testing, and the emergency use authorization process. This manuscript summarizes the diagnostic laboratory and industry perspectives on these issues that were presented and discussed at CMO and proposes some steps that could be taken to improve future pandemic responses.

Retrospective evaluation of clinical decision support for within-laboratory optimization of SARS-CoV-2 NAAT workflow.

The unprecedented demand for severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) testing led to challenges in prioritizing and processing specimens efficiently. We describe and evaluate a novel workflow using provider- and patient-facing ask at order entry (AOE) questions to generate distinctive icons on specimen labels for within-laboratory clinical decision support (CDS) for specimen triaging. A multidisciplinary committee established target turnaround times (TATs) for SARS-CoV-2 nucleic acid amplification test (NAAT) based on common clinical scenarios. A set of AOE questions was used to collect relevant clinical information that prompted icon generation for triaging SARS-CoV-2 NAAT specimens. We assessed the collect-to-verify TATs among relevant clinical scenarios. Our study included a total of 1,385,813 SARS-CoV-2 NAAT conducted from March 2020 to June 2022. Most testing met the TAT targets established by institutional committees, but deviations from target TATs occurred during periods of high demand and supply shortages. Median TATs for emergency department (ED) and inpatient specimens and ambulatory pre-procedure populations were stable over the pandemic. However, healthcare worker and other ambulatory test TATs varied substantially, depending on testing volume and community transmission rates. Median TAT significantly differed throughout the pandemic for ED and inpatient clinical scenarios, and there were significant differences in TAT among label icon-signified ambulatory clinical scenarios. We describe a novel approach to CDS for triaging specimens within the laboratory. The use of CDS tools could help clinical laboratories prioritize and process specimens efficiently, especially during times of high demand. Further studies are needed to evaluate the impact of our CDS tool on overall laboratory efficiency and patient outcomes. IMPORTANCE We describe a novel approach to clinical decision support (CDS) for triaging specimens within the clinical laboratory for severe acute respiratory syndrome coronavirus 2 (SARS­CoV­2) nucleic acid amplification tests (NAAT). The use of our CDS tool could help clinical laboratories prioritize and process specimens efficiently, especially during times of high demand. There were significant differences in the turnaround time for specimens differentiated by icons on specimen labels. Further studies are needed to evaluate the impact of our CDS tool on overall laboratory efficiency and patient outcomes.

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.

Choice Architecture to Assist Clinicians with Appropriate COVID-19 Test Ordering.

BACKGROUND: Despite improving supplies, SARS-CoV-2 nucleic acid amplification tests remain limited during surges and more so given concerns around COVID-19/influenza co-occurrence. Matching clinical guidelines to available supplies ensures resources remain available to meet clinical needs. We report a change in clinician practice after an electronic health record (EHR) order redesign to impact emergency department (ED) testing patterns. METHODS: We included all ED visits between December 1, 2021 and January 18, 2022 across a hospital system to assess the impact of EHR order changes on provider behavior 3 weeks before and after the change. The EHR order redesign included embedded symptom-based order guidance. Primary outcomes were the proportion of COVID-19 + flu/respiratory syncytial virus (RSV) testing performed on symptomatic, admitted, and discharged patients, and the proportion of COVID-19 + flu testing on symptomatic, discharged patients. RESULTS: A total of 52 215 ED visits were included. For symptomatic, discharged patients, COVID-19 + flu/RSV testing decreased from 11.4 to 5.8 tests per 100 symptomatic visits, and the rate of COVID-19 + flu testing increased from 7.4 to 19.1 before and after the intervention, respectively. The rate of COVID-19 + flu/RSV testing increased from 5.7 to 13.1 tests per 100 symptomatic visits for symptomatic patients admitted to the hospital. All changes were significant (P < 0.0001). CONCLUSIONS: A simple EHR order redesign was associated with increased adherence to institutional guidelines for SARS-CoV-2 and influenza testing amidst supply chain limitations necessitating optimal allocation of scarce testing resources. With continually shifting resource availability, clinician education is not sufficient. Rather, system-based interventions embedded within exiting workflows can better align resources and serve testing needs of the community.

Advances in molecular infectious diseases testing in the time of COVID-19.

The Coronavirus Disease of 2019 (COVID-19) pandemic has been a challenging event for laboratory medicine and diagnostics manufacturers. We have had to confront numerous unique and previously unthinkable issues on a daily basis in order to continue offering diagnostic testing for not only Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), but other testing that was significantly impacted by supply chain and staffing disruptions related to COVID-19. Out of this tremendously stressful and, at times, chaotic environment, decades of innovations and advances in testing methodologies and instrumentation became essential to handle the overwhelming volume of samples with clinically appropriate turn-around-time. Additionally, a number of novel testing approaches and technological innovations emerged to address laboratory and public health needs for widespread testing. In this review we consider both technological advances in infectious diseases testing and other innovations in sample collection, processing, automation, workflow, and testing that have embodied the laboratory response to the COVID-19 pandemic.

Implementation of Pre-Admission Caregiver Testing for COVID-19.

BACKGROUND: Caregivers are often at the bedside of hospitalized children posing an additional risk for coronavirus disease 2019 (COVID-19) transmission. We describe the implementation of caregiver COVID-19 testing before inpatient pediatric admissions and the effect on patient cohorting and bed capacity. METHODS: We implemented an ordering pathway to facilitate COVID-19 testing of caregivers of patients admitted to the inpatient units from the pediatric emergency department, elective procedural admissions, or direct admissions at a tertiary children's hospital in the Northeastern United States in August 2021. Testing was expedited by the clinical laboratory, and caregiver results were used to inform cohorting, infection prevention, and bed management decisions. RESULTS: From August 2021 to January 2022, 2558 caregiver tests were ordered through this pathway, and 83 (3.2%) were positive. Of the positive tests, 72 (86.7%) occurred after December 18, 2021, coinciding with the local Omicron variant wave. Among positives, 67 caregiver or child pairs were identified, and 36 positive caregivers had a COVID-19 negative child leading to use of isolation precautions. Reintroduction of patient cohorting increased overall bed capacity from 74% to 100% of available beds. CONCLUSIONS: The overall incidence of COVID-19 among caregivers before admission correlated well with rates of COVID-19 positivity among asymptomatic adults in the community during the study period. Implementation of caregiver testing increased bed capacity by reintroducing cohorting of patients and identified patients needing isolation that would have been missed by patient testing alone. More research is necessary to determine the extent that routine caregiver testing mitigates the risk of nosocomial severe acute respiratory syndrome coronavirus 2 transmission.

Assessment of polymicrobial interactions in bacterial isolates from transfused platelet units associated with sepsis.

BACKGROUND: In 2019 the Centers for Disease Control and Prevention (CDC) reported a series of 4 transfusion reactions that resulted from contamination of apheresis platelet products. Products involved in all 4 cases were contaminated with Acinetobacter calcoaceticus-baumannii complex (ACBC) and in 3 products Staphylococcus saprophyticus was found as well. CDC investigation found that bacterial isolates from the cases were genetically related and suggested a common source of contamination. The contamination of blood products with ACBC is rare and polymicrobial contamination of blood products even less common. ACBC and S. saprophyticus have been observed to adhere to one another and sediment out of suspension in vitro, a process referred to as coaggregation, and we hypothesized that there was an interaction between the strains from these cases that contributed to their co-contamination of blood products. STUDY DESIGN AND METHODS: To test the hypothesis of bacterial interaction, we performed coaggregation experiments and observed the growth characteristics of ACBC and S. saprophyticus strains recovered from contaminated blood products involved in a subset of the CDC cases. RESULTS: An increase in S. saprophyticus CFU concentration was observed after several days of co-culture with ACBC in LB and plasma; however, no other findings suggested coaggregation or augmentative growth interaction between the bacterial strains. CONCLUSION: Ultimately, an interaction between ACBC and S. saprophyticus that could help explain their co-occurrence and growth in contaminated platelet units was not found; however future studies of potential interactions may be warranted.

Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1.

Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas ® SARS-CoV-2 assays, defined by a ≥2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.

Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.

SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat posed by a new variant is essential for adapting response efforts when community transmission is detected. In this study, we compare the dynamics of two variants, Alpha and Iota, by integrating genomic surveillance data to estimate the effective reproduction number (Rt) of the variants. We use Connecticut, United States, in which Alpha and Iota co-circulated in 2021. We find that the Rt of these variants were up to 50% larger than that of other variants. We then use phylogeography to show that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of Alpha were larger than those resulting from Iota introductions. By monitoring the dynamics of individual variants throughout our study period, we demonstrate the importance of routine surveillance in the response to COVID-19.

Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1.

Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.

Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons.

Background: The SARS-CoV-2 Omicron variant became a global concern due to its rapid spread and displacement of the dominant Delta variant. We hypothesized that part of Omicron's rapid rise was based on its increased ability to cause infections in persons that are vaccinated compared to Delta. Methods: We analyzed nasal swab PCR tests for samples collected between December 12 and 16, 2021, in Connecticut when the proportion of Delta and Omicron variants was relatively equal. We used the spike gene target failure (SGTF) to classify probable Delta and Omicron infections. We fitted an exponential curve to the estimated infections to determine the doubling times for each variant. We compared the test positivity rates for each variant by vaccination status, number of doses, and vaccine manufacturer. Generalized linear models were used to assess factors associated with odds of infection with each variant among persons testing positive for SARS-CoV-2. Findings: For infections with high virus copies (Ct < 30) among vaccinated persons, we found higher odds that they were infected with Omicron compared to Delta, and that the odds increased with increased number of vaccine doses. Compared to unvaccinated persons, we found significant reduction in Delta positivity rates after two (43.4%-49.1%) and three vaccine doses (81.1%), while we only found a significant reduction in Omicron positivity rates after three doses (62.3%). Conclusion: The rapid rise in Omicron infections was likely driven by Omicron's escape from vaccine-induced immunity. Funding: This work was supported by the Centers for Disease Control and Prevention (CDC).

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.

The SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40%-80% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant's respective emergence period, finding that Delta emerged 1.37-2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63%-167% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95% CI 3.1-10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta's enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability.

Rectal screening for azole non-susceptible Candida species in patients undergoing liver transplantation.

INTRODUCTION: Candidiasis is the most common invasive fungal infection in solid organ transplant recipients, and liver transplant (LT) recipients are at heightened risk. We hypothesized that pre-transplant screening for azole non-susceptible Candida (ANSC) allows for tailored antifungal prophylaxis to reduce the incidence of post-LT ANSC infection. METHODS: We performed a retrospective chart review of adult (age ≥18 years) patients who underwent LT at Yale New Haven Hospital from April 2019 to March 2021. Screening for ANSC, defined as Candida glabrata or Candida krusei, was performed using a rectal swab prior to or at the time of LT. RESULTS: During the study period, ANSC screening was performed in 47 patients who underwent a total of 48 LTs, with 46/48 (96%) primary LTs and two re-transplantations. Ten of 48 screened cases (21%) had ANSC-positive rectal swabs. Only seven of 10 ANSC-colonized patients received appropriate antifungal prophylaxis (i.e., anidulafungin), and one of these seven patients developed candidemia within 30 days of LT. The median number of candidiasis risk factors was one, and 29% of the cohort had two or more risk factors. DISCUSSION: Routine ANSC screening of LT candidates may assist in selecting appropriate antifungal prophylaxis but may be insufficient to prevent infection in those with multiple risk factors for Candida infection.

Quality Management to Improve CSF Gram Stain Turnaround Time.

BACKGROUND: With appropriate turnaround time (TAT), cerebrospinal fluid (CSF) Gram stains can provide rapid, clinically actionable information in patients with meningitis. Monitoring CSF Gram stain TAT at our institution revealed workflow gaps that were causing result reporting delays. We then implemented a new quality management program to improve TAT. METHODS: We reviewed the TAT of all CSF specimens submitted for bacterial culture received between August 1, 2016, and July 31, 2020, and began prospectively monitoring CSF Gram stain TAT in January 2019. We then implemented the following changes in April 2019: (i) monthly reviews of TAT with staff, (ii) hand-off sheets for shift transitions, and (iii) pre- and post-shift walk throughs including centrifuge checks. RESULTS: A total of 6913 samples were included in the analysis. CSF samples with TAT > 60 min decreased from 27.3% to 9.89% (P < 0.0001), and median TAT decreased by 9 min (P < 0.0001) with significantly reduced variability. These changes were sustained throughout the follow-up period across all shifts and shift transitions. CONCLUSIONS: A new monthly quality metric allowed us to track CSF Gram stain TAT, identify barriers to TAT goals, and implement workflow changes that significantly improved TAT without the need for costly interventions.

Real-world assessment of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) nasopharyngeal swab testing in a region with a high burden of coronavirus disease 2019 (COVID-19).

Concerns persist regarding possible false-negative results that may compromise COVID-19 containment. Although obtaining a true false-negative rate is infeasible, using real-life observations, the data suggest a possible false-negative rate of ˜2.3%. Use of a sensitive, amplified RNA platform should reassure healthcare systems.

Universal SARS-CoV-2 Testing of Emergency Department Admissions Increases Emergency Department Length of Stay.

STUDY OBJECTIVE: Our institution experienced a change in SARS-CoV-2 testing policy as well as substantial changes in local COVID-19 prevalence, allowing for a unique examination of the relationship between SARS-CoV-2 testing and emergency department (ED) length of stay. METHODS: This was an observational interrupted time series of all patients admitted to an academic health system between March 15, 2020, and September 30, 2020. Given testing limitations from March 15 to April 24, all patients receiving SARS-CoV-2 tests were symptomatic. On April 24, testing was expanded to all ED admissions. The primary and secondary outcomes were ED length of stay and number needed to test to obtain a positive, respectively. RESULTS: A total of 70,856 patients were cared for in the EDs during the 7-month period. The testing change increased admission length of stay by 1.89 hours (95% confidence interval 1.39 to 2.38). The number needed to test was 2.5 patients and was highest yield on April 1, 2020, when the state positivity rate was 39.7%; however, the number needed to test exceeded 170 patients by Sept 1, 2020, at which point the state positivity rate was 0.5%. CONCLUSION: Although universal SARS-CoV-2 testing of ED admissions may meaningfully support mitigation and containment efforts, the clinical cost of testing all admissions amid low community positivity is notable. In our system, universal ED SARS-CoV-2 testing was associated with a 24% increase in admission length of stay alongside the detection of only 1 positive case every other day. Given the known harms and risks of ED boarding and crowding, solutions must be developed to support regular operational flow while balancing infection prevention needs.

Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant quickly rose to dominance in mid-2021, displacing other variants, including Alpha. Studies using data from the United Kingdom and India estimated that Delta was 40-80% more transmissible than Alpha, allowing Delta to become the globally dominant variant. However, it was unclear if the ostensible difference in relative transmissibility was due mostly to innate properties of Delta's infectiousness or differences in the study populations. To investigate, we formed a partnership with SARS-CoV-2 genomic surveillance programs from all six New England US states. By comparing logistic growth rates, we found that Delta emerged 37-163% faster than Alpha in early 2021 (37% Massachusetts, 75% New Hampshire, 95% Maine, 98% Rhode Island, 151% Connecticut, and 163% Vermont). We next computed variant-specific effective reproductive numbers and estimated that Delta was 58-120% more transmissible than Alpha across New England (58% New Hampshire, 68% Massachusetts, 76% Connecticut, 85% Rhode Island, 98% Maine, and 120% Vermont). Finally, using RT-PCR data, we estimated that Delta infections generate on average ∼6 times more viral RNA copies per mL than Alpha infections. Overall, our evidence indicates that Delta's enhanced transmissibility could be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on the underlying immunity and behavior of distinct populations.