Proceedings of the Clinical Microbiology Open 2023: discussions about pandemic preparedness.

The 4th Clinical Microbiology Open (CMO) took place in Carlsbad, California, on 10 and 11 February 2023. This event facilitated discussion between clinical and public health laboratory directors, government agencies, and industry representatives from the companies that make up ASM's Corporate Council. While many topics were discussed, much of the discussion focused on pandemic preparedness. There were four major questions addressed: (i) When is the perfect the enemy of good in pandemic testing? (ii) What other types of pathogens might cause another pandemic and how would this affect laboratory response? (iii) What research is needed to better understand the effectiveness of the pandemic response? (iv) What have we learned about the utility of self and at-home testing in future pandemics? This review serves as a summary of these discussions.

Characterization of Serum Samples With Discordant Results in 2 Herpes Simplex Virus Type 2 IgG Assays.

BACKGROUND: Our laboratory system tests sera for herpes simplex virus type 2 (HSV-2) IgG using the DiaSorin Liaison chemiluminescent immunoassay (CIA), with the option to confirm positive samples by a laboratory-developed HerpeSelect inhibition assay. As part of the confirmation process, the HerpeSelect HSV-2 IgG enzyme immunoassay (EIA) is performed. This study investigated the relationship between DiaSorin HSV-2 IgG CIA-positive indices and HerpeSelect HSV-2 IgG EIA results. METHODS: HerpeSelect HSV-2 IgG EIA results were compiled for a cohort of consecutive DiaSorin HSV-2 IgG CIA-positive (index ≥1.10) samples. To further characterize DiaSorin CIA-positive samples that were positive (concordant) or negative (discordant) by the HerpeSelect EIA, a separate composite reference study panel was constructed and also tested using the Biokit HSV-2 IgG assay and an HSV-2 IgG inhibition assay developed for the DiaSorin instrument. Samples were classified as DiaSorin HSV-2 IgG true positive or false positive based on a composite reference using HerpeSelect EIA, Biokit, and DiaSorin inhibition results. RESULTS: Of 2305 consecutive DiaSorin HSV-2 IgG CIA-positive samples, 411 (17.8%) were HerpeSelect HSV-2 IgG EIA negative; 343 of 411 (83%) had DiaSorin indices of 1.10 to 3.00. For the composite reference study panel (N = 120), 59 of 60 discordant samples were classified as DiaSorin HSV-2 IgG false positive based on the composite reference, whereas 58 of 60 concordant samples were classified as true positive. CONCLUSIONS: Nearly all DiaSorin HSV-2 IgG CIA-positive but HerpeSelect HSV-2 IgG EIA-negative sera are falsely positive in the DiaSorin CIA. Furthermore, most DiaSorin false-positive samples exhibit low-positive indices, suggesting that guidelines for confirmatory testing should include low-positive samples by CIA and EIA.

Summary of the Fourth Annual American Sexually Transmitted Diseases Association Workshop on Improving Sexually Transmitted Infection Control Efforts Through Cross-Sector Collaboration.

ABSTRACT: The American Sexually Transmitted Diseases Association has, for several years, been conducting a cross-sector workshop to bring together a variety of stakeholders to develop ideas for collaboratively improving the sexually transmitted infection control efforts in the United States. In this summary, we share the content of discussions and ideas of the fourth annual workshop for future research and potential changes to practice with a focus on diagnostic capacity.

Trichomonas vaginalis Detection in Urogenital Specimens from Symptomatic and Asymptomatic Men and Women by Use of the cobas TV/MG Test.

Trichomonas vaginalis is a prevalent sexually transmitted infection (STI). Diagnosis has historically relied on either microscopic analysis or culture, the latter being the previous gold standard. However, these tests are not readily available for male diagnosis, generally only perform well for symptomatic women, and are not as sensitive as nucleic acid amplification tests (NAATs). Men are largely asymptomatic but carry the organism and transmit to their sexual partners. This multicenter, prospective study evaluated the performance of the cobas T. vaginalis/Mycoplasma genitalium (TV/MG) assay for detection of T. vaginalis DNA compared with patient infection status (PIS) defined by a combination of commercially available NAATs and culture using urogenital specimens. A total of 2,064 subjects (984 men and 1,080 women, 940 [45.5%] symptomatic, 1,124 [54.5%] asymptomatic) were evaluable. In women, sensitivity ranged from 99.4% (95% confidence interval [CI] 96.8 to 99.9%) using vaginal samples to 94.7% (95% CI 90.2 to 97.2%) in PreservCyt samples. Specificity ranged from 98.9 to 96.8% (95% CI 95.4 to 97.8%). In men, the cobas TV/MG assay was 100% sensitive for the detection of T. vaginalis in both male urine samples and meatal swabs, with specificity of 98.4% in urine samples and 92.5% in meatal swabs. The cobas TV/MG is a suitable diagnostic test for the detection of T. vaginalis, which could support public health efforts toward infection control and complement existing STI programs.

A Laboratory Medicine Best Practices Systematic Review and Meta-analysis of Nucleic Acid Amplification Tests (NAATs) and Algorithms Including NAATs for the Diagnosis of Clostridioides (Clostridium) difficile in Adults.

The evidence base for the optimal laboratory diagnosis of Clostridioides (Clostridium) difficile in adults is currently unresolved due to the uncertain performance characteristics and various combinations of tests. This systematic review evaluates the diagnostic accuracy of laboratory testing algorithms that include nucleic acid amplification tests (NAATs) to detect the presence of C. difficile The systematic review and meta-analysis included eligible studies (those that had PICO [population, intervention, comparison, outcome] elements) that assessed the diagnostic accuracy of NAAT alone or following glutamate dehydrogenase (GDH) enzyme immunoassays (EIAs) or GDH EIAs plus C. difficile toxin EIAs (toxin). The diagnostic yield of NAAT for repeat testing after an initial negative result was also assessed. Two hundred thirty-eight studies met inclusion criteria. Seventy-two of these studies had sufficient data for meta-analysis. The strength of evidence ranged from high to insufficient. The uses of NAAT only, GDH-positive EIA followed by NAAT, and GDH-positive/toxin-negative EIA followed by NAAT are all recommended as American Society for Microbiology (ASM) best practices for the detection of the C. difficile toxin gene or organism. Meta-analysis of published evidence supports the use of testing algorithms that use NAAT alone or in combination with GDH or GDH plus toxin EIA to detect the presence of C. difficile in adults. There is insufficient evidence to recommend against repeat testing of the sample using NAAT after an initial negative result due to a lack of evidence of harm (i.e., financial, length of stay, or delay of treatment) as specified by the Laboratory Medicine Best Practices (LMBP) systematic review method in making such an assessment. Findings from this systematic review provide clarity to diagnostic testing strategies and highlight gaps, such as low numbers of GDH/toxin/PCR studies, in existing evidence on diagnostic performance, which can be used to guide future clinical research studies.

Evaluation of Transport Media and Specimen Transport Conditions for the Detection of SARS-CoV-2 by Use of Real-Time Reverse Transcription-PCR.

The global coronavirus (CoV) disease 2019 (COVID-19) pandemic has resulted in a worldwide shortage of viral transport media and raised questions about specimen stability. The objective of this study was to determine the stability of severe acute respiratory syndrome CoV 2 (SARS-CoV-2) RNA in specimen transport media under various storage conditions. Transport media tested included UTM, UTM-RT, ESwab, M4, and saline (0.9% NaCl). Specimen types tested included nasopharyngeal/oropharyngeal swabs in the above-named transport media, bronchoalveolar lavage (BAL) fluid, and sputum. A high-titer SARS-CoV-2 remnant patient specimen was spiked into pooled SARS-CoV-2 RNA-negative specimen remnants for the various medium types. Aliquots of samples were stored at 18°C to 26°C, 2°C to 8°C, and -10°C to -30°C and then tested at time points up to 14 days. Specimens consistently yielded amplifiable RNA with mean cycle threshold differences of <3 over the various conditions assayed, thus supporting the use and transport of alternative collection media and specimen types under a variety of temperature storage conditions.

Detection of SARS-CoV-2 IgG Targeting Nucleocapsid or Spike Protein by Four High-Throughput Immunoassays Authorized for Emergency Use.

A total of 1,200 serum samples that were tested for SARS-CoV-2 IgG antibody using the Abbott Architect immunoassay targeting the nucleocapsid protein were run in 3 SARS-CoV-2 IgG immunoassays targeting spike proteins (DiaSorin Liaison, Ortho Vitros, and Euroimmun). Consensus-positive and consensus-negative interpretations were defined as qualitative agreement in at least 3 of the 4 assays. Agreement of the 4 individual assays with a consensus-negative interpretation (n = 610) ranged from 96.7% to 100%, and agreement with a consensus-positive interpretation (n = 584) ranged from 94.3% to 100%. Laboratory-developed inhibition assays were utilized to evaluate 49 consensus-negative samples that were positive in only one assay; true-positive reactivity was confirmed in only 2 of these 49 (4%) samples. These findings demonstrate very high levels of agreement among 4 SARS-CoV-2 IgG assays authorized for emergency use, regardless of antigen target or assay format. Although false-positive reactivity was identified, its occurrence was rare (no more than 1.7% of samples for a given assay).

Mycoplasma genitalium Detection in Urogenital Specimens from Symptomatic and Asymptomatic Men and Women by Use of the cobas TV/MG Test.

Mycoplasma genitalium (MG) infections are a growing concern within the field of sexually transmitted infections. However, diagnostic assays for M. genitalium have been limited in the United States. As most infections are asymptomatic, individuals can unknowingly pass the infection on, and the prevalence is likely to be underestimated. Diagnosis of M. genitalium infection is recommended using a nucleic acid test. This multicenter study assessed the performance of the cobas Trichomonas vaginalis (TV)/MG assay (cobas) for the detection of M. genitalium, using 22,150 urogenital specimens from both symptomatic and asymptomatic men and women collected at geographically diverse sites across the United States. The performance was compared to a reference standard of three laboratory-developed tests (LDTs). The specificity of the cobas assay for M. genitalium ranged from 96.0% to 99.8% across symptomatic and asymptomatic men and women. The sensitivities in female vaginal swabs and urine samples were 96.6% (95% confidence interval [CI], 88.5 to 99.1%) and 86.4% (95% CI, 75.5 to 93.0%), respectively. The sensitivities in male urine and meatal swab samples were 100% (95% CI, 94.0 to 100%) and 85.0% (95% CI, 73.9 to 91.9%), respectively. This study demonstrated that the cobas assay was highly sensitive and specific in all relevant clinical samples for the detection of M. genitalium.

Evaluation of the Performance of the Cobas CT/NG Test for Use on the Cobas 6800/8800 Systems for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Male and Female Urogenital Samples.

The clinical performance of the Cobas CT/NG assay on the Cobas 6800/8800 systems (Cobas) for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae was established in a multisite, prospective collection study using male and female urogenital specimens; supportive data from archived specimens were also included. The results obtained with the Cobas assay were compared with the patient infected status derived from a combination of U.S. Food and Drug Administration-approved nucleic acid amplification tests to determine the sensitivity and specificity of detection from each sample type. The sensitivity of Cobas for the detection of C. trachomatis in female specimens was 95.6% (95% confidence interval [CI], 92.4% to 97.4%) for urine; 98.6% (95% CI, 95.2% to 99.6%) and 99.2% (95% CI, 95.4% to 99.9%) for clinician- and self-collected vaginal swab specimens, respectively; 93.3% (95% CI, 89.6% to 95.7%) for endocervical swabs; and 92.5% (95% CI, 88.7% to 95.1%) for cervical swab samples in PreservCyt. The specificity for the detection of C. trachomatis was ≥98.8% for all female sample types. Sensitivity and specificity estimates of Cobas for the detection of C. trachomatis in male urine samples were 100% (96.8% to 100.0%) and 99.7% (95% CI, 99.2% to 99.9%), respectively. The sensitivity of Cobas for the detection of N. gonorrhoeae in female specimens was 94.8% (95% CI, 89.6% to 97.4%) for urine; 100.0% (95% CI, 87.9% to 100.0%) and 100.0% (95% CI, 87.9% to 100.0%) for clinician- and self-collected vaginal swab specimens, respectively; 97.0% (95% CI, 91.5% to 99.0%) for endocervical swabs; and 96.6% (95% CI, 90.6% to 98.8%) for cervical samples in PreservCyt; the specificity for all female sample types was >99.0%. The sensitivity and specificity of Cobas for detecting N. gonorrhoeae in male urine were 100.0% (95% CI, 95.8% to 100.0%) and 99.5% (95% CI, 98.8% to 99.8%), respectively. Fully automated assays help fill the clinical need for a sensitive, high-throughput screening tool to aid public health efforts to control C. trachomatis and N. gonorrhoeae infections.

High-volume workflow and performance comparisons for Chlamydia trachomatis and Neisseria gonorrhoeae testing using automated molecular platforms.

BACKGROUND: The global burden of sexually transmitted infections (STIs) is high and there have been reports of increasing chlamydial and gonorrheal infections. High-volume screening programs for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are an important component of STI control. This study evaluated the high-volume workflow and performance of the cobas® CT/NG assay for use on the automated Roche cobas® 6800 system, with the cobas p 480 instrument for pre-analytics, compared with the Aptima Combo 2 assay on the Hologic Panther system. METHODS: High-volume workflow and performance were evaluated using paired female urine specimens. Workflow analysis (n = 376) included hands-on time (HoT), number of manual interventions, and time to first and last results. For performance assessment, paired results from the cobas CT/NG and Aptima Combo 2 assays, for both CT and NG, were compared and two-sided 95% confidence intervals calculated to provide estimates of positive percent agreement (PPA), negative percent agreement (NPA), and overall percent agreement (OPA) between the tests. McNemar's test was used for significance testing. RESULTS: Pre-analytical preparations and system start-up on the cobas 6800 system required 00:27:38 (hr:min:sec) HoT whilst the Panther system required 00:30:43. The cobas 6800 system required eight interactions and 00:43:59 HoT to process 376 samples. The Panther system required six interactions and 00:39:10 HoT. Time to first results was 02:53:00 on the cobas c6800 system for 96 samples and 03:28:29 on the Panther system for five samples. The cobas 6800 system delivered all 376 results 3 h faster than the Panther system (07:45:26 and 10:47:30, respectively). The performance correlation between both assays was high (PPA, NPA and OPA > 99% for both CT and NG). McNemar's test revealed no statistically significant difference between the assays. CONCLUSION: For high-volume automated CT/NG testing, both the cobas 6800 system and Panther system provided accurate results. Although less manual intervention steps were needed for the Panther system, improved turnaround time was obtained with the cobas 6800 system with less risk for contamination. The additional testing capacity on the cobas 6800 system would allow a growing service to deliver more results in a single shift.

Right-Sizing Technology in the Era of Consumer-Driven Health Care.

Technology for modern clinical and public health microbiology laboratories has evolved at an impressive rate over the last two decades. Contemporary diagnostics can rapidly provide powerful data that can impact patient lives and support infectious disease outbreak investigations. At the same time, dramatic changes to health care delivery are putting new pressures on a system that is now focusing on patient-centric, value-driven, convenient care. For laboratories, balancing all these demands in a cost-contained environment remains a challenge. This article explores the current and future directions of diagnostics in our dynamic health care environment.

Infants 1-90 days old hospitalized with human rhinovirus infection.

BACKGROUND: Human rhinovirus (HRV) is a common cause of respiratory illness in children. The impact of HRV infection on 1- to 90-day-old infants is unclear. We hypothesized that HRV infection would be clinically similar to respiratory syncytial virus (RSV) infection in the hospitalized infants. METHODS: We conducted a retrospective study of hospitalized infants, who were 1-90 days old, with HRV or RSV within the Southern California Kaiser Permanente network over a 1-year period (August 2010 to October 2011). RESULTS: We identified 245 hospitalized infants who underwent respiratory virus testing. HRV was found in 52 infants (21%) compared to 79 infants (32%) with RSV (P = 0.008). Infants with HRV infection experienced longer hospital stays compared to those with RSV (median length of stay 4 days vs. 3 days, P = 0.009) and had fewer short hospital stays ≤3 days (P = 0.029). There was a trend in infants with HRV infection to be younger (P = 0.071) and have more fevers (P = 0.052). CONCLUSIONS: Recent advances in diagnostics allow for identification of a broad range of viral pathogens in infants. Compared to RSV, HRV was associated with longer hospital stays. Additional studies and improved, more specific testing, methods are needed to further define the effects of HRV infection in infants 1-90 days old.

Rapid and Accurate Identification of SARS-CoV-2 Variants Using Real Time PCR Assays.

Background: Genomic surveillance efforts for SARS-CoV-2 are needed to understand the epidemiology of the COVID-19 pandemic. Viral variants may impact routine diagnostic testing, increase viral transmissibility, cause differences in disease severity, have decreased susceptibility to therapeutics, and/or confer the ability to evade host immunity. While viral whole-genome sequencing (WGS) has played a leading role in surveillance programs, many laboratories lack the expertise and resources for performing WGS. This study describes the performance of multiplexed real-time reverse transcription-PCR (RT-PCR) assays for identification of SARS-CoV-2 variants. Methods: SARS-CoV-2 specimens were tested for spike-gene variants using a combination of allele-specific primer and allele-specific detection technology (PlexPrime® and PlexZyme®). Targeted detection of spike gene mutations by RT-PCR was compared to variant detection in positive specimens by WGS, including the recently emerged SARS-CoV-2 Omicron variant. Results: A total of 398 SAR-CoV-2 RT-PCR positive and 39 negative specimens previously tested by WGS were re-tested by RT-PCR genotyping. PCR detection of spike gene mutations N501Y, E484K, and S982A correlated 100% with WGS for the 29 lineages represented, including Alpha (B.1.1.7), Beta (B.1.351), and Gamma (P.1). Incorporating the P681R spike gene mutation also allowed screening for the SARS-CoV-2 Delta variant (B.1.617.2 and AY sublineages). Further sampling of 664 specimens that were screened by WGS between June and August 2021 and then re-tested by RT-PCR showed strong agreement for Delta variant positivity: 34.5% for WGS vs 32.9% for RT-PCR in June; 100% vs 97.8% in August. In a blinded panel of 16 Omicron and 16 Delta specimens, results of RT-PCR were 100% concordant with WGS results. Conclusions: These data demonstrate that multiplexed real-time RT-PCR genotyping has strong agreement with WGS and may provide additional SARS-CoV-2 variant screening capabilities when WGS is unavailable or cost-prohibitive. RT-PCR genotyping assays may also supplement existing sequencing efforts while providing rapid results at or near the time of diagnosis to help guide patient management.

Transience of interference in an immunoassay measuring serum levels of beta-D-glucan.

Some sera tested for 1-3-beta-D-glucan to identify invasive fungal infections exhibit interference. To assess interference transience, we evaluated results for 426 patients with an interference sample followed by a later sample. Interference was transient for 73% of patients (later sample negative or positive); median time between samples was 8 days.

Evaluation of the Cepheid Xpert MTB/RIF assay for direct detection of Mycobacterium tuberculosis complex in respiratory specimens.

A total of 217 specimens submitted for routine smear and culture from three different sites within the western United States were used to evaluate the GeneXpert MTB/RIF assay (for research use only) (Cepheid, Sunnyvale, CA). Overall agreement compared to culture was 89% (98% for smear positives and 72% for smear negatives) for detection of Mycobacterium tuberculosis.

Relationship between DiaSorin Liaison Treponema pallidum antibody indices and confirmatory assay results in the reverse syphilis testing algorithm.

Published studies show that >99% of sera reactive in the reverse syphilis testing algorithm (RSTA) screening assay with an index above an assay-specific threshold confirm as reactive, with either a rapid plasma reagin-reactive (RPRR) or RPR-nonreactive/Treponema pallidum particle agglutination-reactive (TPPAR) result. However, the relationship between screen indices and confirmatory patterns has not been characterized. We thus assessed confirmatory testing results for 577 sera submitted for RSTA testing and a screen-reactive result in the DiaSorin Liaison assay. The median screen index was significantly higher for RPRR samples than TPPAR samples (55.6 versus 10.4), and the proportion with indices >28.3 (median for all 577 samples) was significantly higher for RPRR versus TPPAR samples (82% versus 26%). However, RPRR titers did not significantly correlate with screen indices (R2 = 0.02). These findings demonstrate a significant relationship between RSTA screen indices and confirmatory assay results. The clinical utility of this relationship requires further study.

Relationship between hepatitis C virus (HCV) IgG index values and quantitative HCV RNA results in HCV IgG-reactive serum samples.

Centers for Disease Control guidelines recommend hepatitis C virus (HCV) RNA testing of all HCV IgG-reactive samples, although earlier studies found that IgG-reactive samples with low indices were negative in qualitative RNA assays. To determine if previous study results could be confirmed using current real-time RT-PCR technology, we investigated the relationship between HCV IgG index (Ortho VITROS) and quantitative HCV RNA results (cobas HCV) for 2368 consecutive IgG-reactive sera. Results were segregated into Low (1.00-16.0), Medium (16.1-30.0), and High (>30.0) IgG index groups. Although median viral load (VL) of RNA-positive samples was similar in all 3 groups, the percentage with low VL (1.18-4.16 log IU/mL) was increased for the Low group. Further analysis of the Low group revealed that 23 of 370 (6%) samples with IgG indices ≤8.00 were RNA-positive, and 13/23 (57%) had low VL. Our analysis supports the Centers for Disease Control recommendation to test all HCV IgG-reactive sera for HCV RNA.