Viral load and infectivity of SARS-CoV-2 in paired respiratory and oral specimens from symptomatic, asymptomatic or post-symptomatic individuals

In the present study, we assessed the diagnostic sensitivity and determined the viral load and infectivity of SARS-CoV-2 in paired respiratory (nasopharyngeal and anterior nares) and oral samples (saliva and sublingual swab). Samples were collected from 77 individuals of which 75 were diagnosed with COVID-19 and classified as symptomatic (n=29), asymptomatic (n=31), or post-symptomatic (n=15). Specimens were collected at one time point from each individual, between day 1 to 23 after the initial COVID-19 diagnosis, and included self-collected saliva (S), or sublingual (SL) swab, and bilateral anterior nares (AN) swab, followed by healthcare provider collected nasopharyngeal (NP) swab. Sixty-three specimen sets were tested using five assay/platforms. The diagnostic sensitivity of each assay/platform and specimen type was determined. Of the 63 specimen sets, SARS-CoV-2 was detected in 62 NP specimens, 52 AN specimens, 59 saliva specimens, and 31 SL specimens by at least one platform. Infectious SARS-CoV-2 was isolated from 21 NP, 13 AN, 12 saliva, and one SL specimen out of 50 specimen sets. SARS-CoV-2 isolation was most successful up to 5 days after initial COVID-19 diagnosis using NP specimens from symptomatic patients (16 of 24 positives, 66.67%), followed by specimens from asymptomatic patients (5 of 17 positives, 29.41%), while it was not very successful with specimens from post-symptomatic patients. Benefits of self-collected saliva and AN specimens balance the loss of sensitivity relative to NP specimens. Therefore, saliva and AN specimens are acceptable alternatives for symptomatic SARS-CoV-2 diagnostic testing or surveillance with increased sampling frequency of asymptomatic individuals.

979. Getting Candid with Candida auris: Evaluation of Isolates at SBH Health System

Background Candida auris is a multidrug resistant yeast that was originally isolated in the external ear of a patient in Japan in 2009. Since then, it has rapidly spread throughout the world. C. auris is inherently a multidrug resistant organism, making echinocandins the drugs of choice. C. auris was first isolated in SBH in a wound culture in 2018, and it has become a major health concern. Our objectives were to evaluate our clinical C. auris isolates, identify potential risk factors for infection, and assess our susceptibilities to determine the most appropriate treatment option. Methods This was a retrospective chart review of all clinical isolates of C. auris from July 2018 – April 2021. Data collection included location prior to admission, SBH hospitalization within 90 days, hospital vs community acquired, new vs recurrent, specimen type, susceptibilities, and lines at the time of culture. Results A total of 121 clinical isolates were evaluated from 74 patients. Although initially clinical isolates were rare, prevalence increased in subsequent years, with 97 clinical isolates identified in 2020. Isolates were identified in various specimen types, with the majority in urine, respiratory samples, or blood cultures. 64% of the isolates were hospital onset. Among patients who tested positive for C. auris colonization through surveillance testing, 22% proceeded to develop clinical infections. Most of the patients with positive blood cultures had either one or multiple IV access points, which may be a risk factor for candidemia. All isolates were resistant to fluconazole, 87% were susceptible to amphotericin B, and susceptibility to echinocandins ranged from 98-99%. Susceptibilities Susceptibilities for the Candida auris clinical isolates received from the NYS Department of Health Specimen Type IV Access in Positive Blood Cultures Access points that were present at the time of candidemia Conclusion Candida auris is a persistent fungus that is highly contagious that has been increasing in prevalence. Infection control measures remain the most proven method to decrease the development of clinical infections. Our study has some limitations, such as the retrospective design, the lack of a control group, lack of clinical outcomes, and limited surveillance testing capabilities. C. auris remains a major cause of concern for nosocomial infections, particularly in patients with various indwelling catheters. Our susceptibilities confirmed echinocandins as the class of choice for treatment of C. auris infections. Disclosures Judith Berger, MD, Nothing to disclose

Utilization of 2D Barcode Technology to Create Surgical Pathology Reports

Introduction/Objective After professional transcription service is eliminated, pathologists inevitably undertake the task of diagnostic data entry into pathology repot by adapting a variety of methods such as speech recognition, manual typing, and pre-texted command. Errors and inefficiency in reporting remain common problems, especially for information with unusual syntax such as genotype or nucleotide sequences. To overcome these shortcomings, we introduce here a novel application of a well-established technology as a complementary method, namely 2- dimensional (2D) barcode symbology. Methods/Case Report Commonly used diagnostic wordings of pathology reports including specimen type, surgical procedure, diagnosis, and test results are collated and organized by organ (specimen type) and by their frequency of usage/occurrence. Next, 2D data matrix barcodes are created for these diagnostic wordings using a on-line tool (www.free-barcode-generator.net/datamatrix/). The 2D barcodes along with their text are displayed on the computer screen (or printed out as a booklet). A 2D barcode scanner (Symbol LS2208, Motorola) was used to retrieve the text information from the barcodes and transfer into the pathology report. To assess the efficacy of this barcode method, we evaluated the time of data entry into reports for 117 routine cases using an on-line stopwatch and compared with those by other data entry methods. Results (if a Case Study enter NA) Unlike manual typing or speech recognition, the barcode method did not introduce typographic or phonosemantic errors since the method simply transferred pre-texted and proof-read text content to report. It was also faster than manual typing or speech recognition, and its speed was comparable to that of the pre-text method integrated in LIS but did not require human memorization of innumerable text commands to retrieve desired diagnosis wordings. Conclusion Our preliminary results demonstrated that the diagnostic data entry time was reduced from 28.5% by other methods to 22.1% by the barcode method although due to the small sample size, statistical analysis was not conclusive.

Performance of self-collected anterior nasal swabs and saliva specimens for detection of SARS-COV-2 during symptomatic and asymptomatic periods

Background Anterior nasal swabs (ANS) are established specimen collection methods for SARS-CoV-2 infection detection. While saliva (SA) specimens provide an alternative, few studies have comprehensively characterized the performance of SA specimens in longitudinal studies. Methods We compared SARS-CoV-2 detections between paired self-collected ANS and SA specimens from a household transmission study. Participants recorded symptoms and paired ANS and SA specimens daily for 14 days. Specimens were tested using RT-PCR. We calculated the proportion of detections identified by each specimen type among the detections from both types combined. We computed percent agreement and Kappa statistics to assess concordance in detections. We also computed estimates stratified by presence of symptoms, and examined the influence of traditional and inactivating transport media on the performance of ANS. Results We examined 2535 self-collected paired specimens from 216 participants. Among 1,238(49%) paired specimens with detections by either specimen type, ANS identified 77.1%[954](95%CI: 74.6–79.3%) and SA 81.9%[1014](79.7–84.0%), with a difference of 4.9%(1.4–8.5%). Overall agreement was 80.0% and Kappa was 0.6(0.5-0.6). Nevertheless, the difference in the proportion of detections identified by ANS and SA using traditional and inactivating transport media was 32.5%(26.8–38.0) and −9.5%(−13.7– -5.2), respectively. Among participants who remained asymptomatic, the difference in detections between SA and ANS was 51.2%(31.8–66.0) and 26.1%(0–48.5) using traditional and inactivating media, respectively. Conclusion Self-collected saliva specimens provide a non-invasive alternative to nasal swabs, especially to those collected in traditional transport media, for longitudinal field studies that aim to detect both symptomatic and asymptomatic SARS-CoV-2 infections.

Coming up short: Comparing venous blood, dried blood spots & saliva samples for measuring telomere length in health equity research

Background Telomere length (TL) in peripheral blood mononuclear cells (PBMC) from fresh venous blood is increasingly used to estimate molecular impacts of accumulated social adversity on population health. Sometimes, TL extracted from saliva or dried blood spots (DBS) are substituted as less invasive and more scalable specimen collection methods; yet, are they interchangeable with fresh blood? Studies find TL is correlated across tissues, but have not addressed the critical question for social epidemiological applications: Do different specimen types show the same association between TL and social constructs? Methods We integrate expertise in social epidemiology, molecular biology, and the statistical impact of measurement error on parameter estimates. Recruiting a diverse sample of 132 Metro-Detroit women, we measure TL for each woman from fresh blood PBMC, DBS, and saliva. Using regression methods, we estimate associations between social characteristics and TL, comparing estimates across specimen types for each woman. Results Associations between TL and social characteristics vary by specimen type collected from the same woman, sometimes qualitatively altering estimates of the magnitude or direction of a theorized relationship. Being Black is associated with shorter TL in PBMC, but longer TL in saliva or DBS. Education is positively associated with TL in fresh blood, but negatively associated with TL using DBS. Conclusion Findings raise concerns about the use of TL measures derived from different tissues in social epidemiological research. Investigators need to consider the possibility that associations between social variables and TL may be systematically related to specimen type, rather than be valid indicators of socially-patterned biopsychosocial processes.

Patterns of SARS-CoV-2 Testing Preferences in a National Cohort in the United States: Latent Class Analysis of a Discrete Choice Experiment (Preprint)

BACKGROUND Inadequate screening and diagnostic testing in the United States throughout the first several months of the COVID-19 pandemic led to undetected cases transmitting disease in the community and an underestimation of cases. Though testing supply has increased, maintaining testing uptake remains a public health priority in the efforts to control community transmission considering the availability of vaccinations and threats from variants. OBJECTIVE This study aimed to identify patterns of preferences for SARS-CoV-2 screening and diagnostic testing prior to widespread vaccine availability and uptake. METHODS We conducted a discrete choice experiment (DCE) among participants in the national, prospective CHASING COVID (Communities, Households, and SARS-CoV-2 Epidemiology) Cohort Study from July 30 to September 8, 2020. The DCE elicited preferences for SARS-CoV-2 test type, specimen type, testing venue, and result turnaround time. We used latent class multinomial logit to identify distinct patterns of preferences related to testing as measured by attribute-level part-worth utilities and conducted a simulation based on the utility estimates to predict testing uptake if additional testing scenarios were offered. RESULTS Of the 5098 invited cohort participants, 4793 (94.0%) completed the DCE. Five distinct patterns of SARS-CoV-2 testing emerged. Noninvasive home testers (n=920, 19.2% of participants) were most influenced by specimen type and favored less invasive specimen collection methods, with saliva being most preferred; this group was the least likely to opt out of testing. Fast-track testers (n=1235, 25.8%) were most influenced by result turnaround time and favored immediate and same-day turnaround time. Among dual testers (n=889, 18.5%), test type was the most important attribute, and preference was given to both antibody and viral tests. Noninvasive dual testers (n=1578, 32.9%) were most strongly influenced by specimen type and test type, preferring saliva and cheek swab specimens and both antibody and viral tests. Among hesitant home testers (n=171, 3.6%), the venue was the most important attribute; notably, this group was the most likely to opt out of testing. In addition to variability in preferences for testing features, heterogeneity was observed in the distribution of certain demographic characteristics (age, race/ethnicity, education, and employment), history of SARS-CoV-2 testing, COVID-19 diagnosis, and concern about the pandemic. Simulation models predicted that testing uptake would increase from 81.6% (with a status quo scenario of polymerase chain reaction by nasal swab in a provider’s office and a turnaround time of several days) to 98.1% by offering additional scenarios using less invasive specimens, both viral and antibody tests from a single specimen, faster turnaround time, and at-home testing. CONCLUSIONS We identified substantial differences in preferences for SARS-CoV-2 testing and found that offering additional testing options would likely increase testing uptake in line with public health goals. Additional studies may be warranted to understand if preferences for testing have changed since the availability and widespread uptake of vaccines.

Sequencing SARS-CoV-2 Genomes from Saliva

Genomic sequencing is crucial to understanding the epidemiology and evolution of SARS-CoV-2. Often, genomic studies rely on remnant diagnostic material, typically nasopharyngeal swabs, as input into whole genome SARS-CoV-2 next-generation sequencing pipelines. Saliva has proven to be a safe and stable specimen for the detection of SARS-CoV-2 RNA via traditional diagnostic assays, however saliva is not commonly used for SARS-CoV-2 sequencing. Using the ARTIC Network amplicon-generation approach with sequencing on the Oxford Nanopore MinION, we demonstrate that sequencing SARS-CoV-2 from saliva produces genomes comparable to those from nasopharyngeal swabs, and that RNA extraction is necessary to generate complete genomes from saliva. In this study, we show that saliva is a useful specimen type for genomic studies of SARS-CoV-2.

Molecular epidemiology of carbapenem-resistant Enterobacterales in Thailand, 2016–2018

Background Carbapenem-resistant Enterobacterales (CRE) is a global threat. Enterobacterales develops carbapenem resistance through several mechanisms, including the production of carbapenemases. We aim to describe the prevalence of Carbapenem-resistant Enterobacterales (CRE) with and without carbapenemase production and distribution of carbapenemase-producing (CP) genes in Thailand using 2016–2018 data from a national antimicrobial resistance surveillance system developed by the Thailand National Institute of Health (NIH). Methods CRE was defined as any Enterobacterales resistant to ertapenem, imipenem, or meropenem. Starting in 2016, 25 tertiary care hospitals from the five regions of Thailand submitted the first CRE isolate from each specimen type and patient admission to Thailand NIH, accompanied by a case report form with patient information. NIH performed confirmatory identification and antimicrobial susceptibility testing and performed multiplex polymerase chain reaction testing to detect CP-genes. Using 2016–2018 data, we calculated proportions of CP-CRE, stratified by specimen type, organism, and CP-gene using SAS 9.4. Results Overall, 4,296 presumed CRE isolates were submitted to Thailand NIH; 3,946 (93%) were confirmed CRE. Urine (n = 1622, 41%) and sputum (n = 1380, 35%) were the most common specimen types, while blood only accounted for 323 (8%) CRE isolates. The most common organism was Klebsiella pneumoniae (n = 2660, 72%), followed by Escherichia coli (n = 799, 22%). The proportion of CP-CRE was high for all organism types (range: 85–98%). Of all CRE isolates, 2909 (80%) had one CP-gene and 629 (17%) had > 1 CP-gene. New Delhi metallo-beta-lactamase (NDM) was the most common CP-gene, present in 2392 (65%) CRE isolates. K. pneumoniae carbapenemase (KPC) and Verona integron-encoded metallo-β-lactamase (VIM) genes were not detected among any isolates. Conclusion CP genes were found in a high proportion (97%) of CRE isolates from hospitals across Thailand. The prevalence of NDM and OXA-48-like genes in Thailand is consistent with pattern seen in Southeast Asia, but different from that in the United States and other regions. As carbapenemase testing is not routinely performed in Thailand, hospital staff should consider treating all patients with CRE with enhanced infection control measures; in line with CDC recommendation for enhanced infection control measures for CP-CRE because of their high propensity to spread.