Detection of SARS-CoV-2 infection in the general population by three prevailing rapid antigen tests: cross-sectional diagnostic accuracy study

BACKGROUND

Rapid antigen diagnostic tests (Ag-RDTs) are the most widely used point-of-care tests for detecting SARS-CoV-2 infection. Since the accuracy may have altered by changes in SARS-CoV-2 epidemiology, indications for testing, sampling and testing procedures, and roll-out of COVID-19 vaccination, we evaluated the performance of three prevailing SARS-CoV-2 Ag-RDTs.

METHODS

In this cross-sectional study, we consecutively enrolled individuals aged >16 years presenting for SARS-CoV-2 testing at three Dutch public health service COVID-19 test sites. In the first phase, participants underwent either BD-Veritor System (Becton Dickinson), PanBio (Abbott), or SD-Biosensor (Roche Diagnostics) testing with routine sampling procedures. In a subsequent phase, participants underwent SD-Biosensor testing with a less invasive sampling method (combined oropharyngeal-nasal [OP-N] swab). Diagnostic accuracies were assessed against molecular testing.

RESULTS

Six thousand nine hundred fifty-five of 7005 participants (99%) with results from both an Ag-RDT and a molecular reference test were analysed. SARS-CoV-2 prevalence and overall sensitivities were 13% (188/1441) and 69% (129/188, 95% CI 62-75) for BD-Veritor, 8% (173/2056) and 69% (119/173, 61-76) for PanBio, and 12% (215/1769) and 74% (160/215, 68-80) for SD-Biosensor with routine sampling and 10% (164/1689) and 75% (123/164, 68-81) for SD-Biosensor with OP-N sampling. In those symptomatic or asymptomatic at sampling, sensitivities were 72-83% and 54-56%, respectively. Above a viral load cut-off (≥5.2 log₁₀ SARS-CoV-2 E-gene copies/mL), sensitivities were 86% (125/146, 79-91) for BD-Veritor, 89% (108/121, 82-94) for PanBio, and 88% (160/182, 82-92) for SD-Biosensor with routine sampling and 84% (118/141, 77-89) with OP-N sampling. Specificities were >99% for all tests in most analyses. Sixty-one per cent of false-negative Ag-RDT participants returned for testing within 14 days (median: 3 days, interquartile range 3) of whom 90% tested positive.

CONCLUSIONS

Overall sensitivities of three SARS-CoV-2 Ag-RDTs were 69-75%, increasing to ≥86% above a viral load cut-off. The decreased sensitivity among asymptomatic participants and high positivity rate during follow-up in false-negative Ag-RDT participants emphasise the need for education of the public about the importance of re-testing after an initial negative Ag-RDT should symptoms develop. For SD-Biosensor, the diagnostic accuracy with OP-N and deep nasopharyngeal sampling was similar; adopting the more convenient sampling method might reduce the threshold for professional testing.

Misidentification of meticillin-resistant Staphylococcus aureus by the Cepheid Xpert MRSA NxG assay, the Netherlands, February to March 2021

We describe two false-negative results in the detection of meticillin-resistant Staphylococcus aureus (MRSA) of sequence type 398 and spa type t011 using the Cepheid Xpert MRSA NxG assay. The isolates were recovered in late February and early March 2021 from two patients in different hospitals in the northern Netherlands. Variations between the two isolate genomes indicate that this MRSA strain might have been spreading for some time and could have disseminated to other regions of the Netherlands and other European countries.

Bacterial agents in vulvovaginitis and vaginal discharge: a 10-year retrospective study in the Netherlands

Vulvovaginitis is a common problem in the GP's practice. Causes are bacterial vaginosis (BV), Candida infection and sexually transmitted infections (STIs). Only if empirical treatment fails, a vaginal swab is sent in for culture and BV detection. However, without culture essential, bacterial pathogens may escape diagnosis. Many molecular BV assays have recently appeared on the marketplace, all quite differing in price and targets. However, for years, the Nugent score has been the gold standard for BV detection. We analysed retrospectively 10 years of microbiology results of vulvovaginal swabs, focusing on less frequently reported bacterial pathogens, and assessed the characteristics of BV diagnostics. Vulvovaginal swabs sent in between 2010 and 2020 from > 11,000 GP patients with vulvovaginitis associated symptoms, but negative STI tests, were analysed. First cultures and repeat cultures after at least 6 months were included in four age groups: < 12, 12-17, 18-51 and > 51 years. Candida species and BV were most frequently found, with the highest prevalence in premenopausal women. Haemophilus influenzae, beta-haemolytic streptococci, Streptococcus pneumoniae and Staphylococcus aureus were isolated in 5.6% of all cultures, with the highest percentages in children and postmenopausal women. If empirical treatment of vulvovaginitis fails, bacterial culture should be performed to detect all potentially pathogenic microorganisms to obtain a higher rate of successful diagnosis and treatment, avoiding unnecessary antimicrobial use and costs. For BV detection, molecular testing may seem attractive, but Nugent scoring still remains the low-cost gold standard. We recommend incorporating the above in the appropriate guidelines.

Epidemiology and Clinical Management of Fusarium keratitis in the Netherlands, 2005-2016

Introduction: Recognizing fungal keratitis based on the clinical presentation is challenging. Topical therapy may be initiated with antibacterial agents and corticosteroids, thus delaying the fungal diagnosis. As a consequence, the fungal infection may progress ultimately leading to more severe infection and blindness. We noticed an increase of fungal keratitis cases in the Netherlands, especially caused by Fusarium species, which prompted us to conduct a retrospective cohort study, aiming to describe the epidemiology, clinical management, and outcome.

Materials and Methods: As fungi are commonly sent to the Dutch mycology reference laboratory for identification and in vitro susceptibility testing, the fungal culture collection was searched for Fusarium isolates from corneal scrapings, corneal swabs, and from contact lens (CL) fluid, between 2005 and 2016. All Fusarium isolates had been identified up to species level through sequencing of the ITS1-5.8S-ITS2 region of the rDNA and TEF1 gene. Antifungal susceptibility testing was performed according to the EUCAST microbroth dilution reference method. Antifungal agents tested included amphotericin B, voriconazole, and natamycin. In addition, susceptibility to the antisepticum chlorhexidine was tested. Ophthalmologists were approached to provide demographic and clinical data of patients identified through a positive culture.

Results: Between 2005 and 2016, 89 cases of Fusarium keratitis from 16 different hospitals were identified. The number of cases of Fusarium keratitis showed a significant increase over time (R² = 0.9199), with one case in the first 5 years (2005–2009) and multiple cases from 2010 and onwards. The male to female ratio was 1:3 (p = 0.014). Voriconazole was the most frequently used antifungal agent, but treatment strategies differed greatly between cases including five patients that were treated with chlorhexidine 0.02% monotherapy. Keratitis management was not successful in 27 (30%) patients, with 20 (22%) patients requiring corneal transplantation and seven (8%) requiring enucleation or evisceration. The mean visual acuity (VA) was moderately impaired with a logMAR of 0.8 (95% CI 0.6–1, Snellen equivalent 0.16) at the time of Fusarium culture. Final average VA was within the range of normal vision [logMAR 0.2 (95% CI 0.1–0.3), Snellen equivalent 0.63]. CL wear was reported in 92.9% of patients with Fusarium keratitis. The time between start of symptoms and diagnosis of fungal keratitis was significantly longer in patients with poor outcome as opposed to those with (partially) restored vision; 22 vs. 15 days, respectively (mean, p = 0.024). Enucleation/evisceration occurred in patients with delayed fungal diagnosis of more than 14 days after initial presentation of symptoms. The most frequently isolated species was F. oxysporum (24.7%) followed by F. solani sensu stricto (18%) and F. petroliphilum (9%). The lowest MICs were obtained with amphotericin B followed by natamycin, voriconazole, and chlorhexidine.

Conclusion: Although Fusarium keratitis remains a rare complication of CL wear, we found a significant increase of cases in the Netherlands. The course of infection may be severe and fungal diagnosis was often delayed. Antifungal treatment strategies varied widely and the treatment failure rate was high, requiring transplantation or even enucleation. Our study underscores the need for systematic surveillance of fungal keratitis and a consensus management protocol.

Revealing the Virulence Potential of Clinical and Environmental Aspergillus fumigatus Isolates Using Whole-Genome Sequencing

Aspergillus fumigatus is considered a common causative agent of human fungal infections. A restricted number of virulence factors have been described, and none of them lead to a differentiation in the virulence level among different strains. Variations in the virulence phenotype depending on the isolate origin, measured as survival percentage in animal infection models, have been previously reported. In this study, we analyzed the whole-genome sequence of A. fumigatus isolates from clinical and environmental origins to determine their virulence genetic content. The sample included four isolates sequenced at the University Medical Center Groningen (UMCG), three clinical (two of them isolated from the same patient) and the experimental strain B5233, and the draft genomes of one reference strain, two environmental and two clinical isolates obtained from a public database. The fungal genomes were screened for the presence of virulence-related genes (VRGs) using an in-house database of 244 genes related to thermotolerance, resistance to immune responses, cell wall formation, nutrient uptake, signaling and regulation, and production of toxins and secondary metabolites and allergens. In addition, we performed a variant calling analysis to compare the isolates sequenced at the UMCG and investigated their genetic relatedness using the TRESP (Tandem Repeats located within Exons of Surface Protein coding genes) genotyping method. We neither observed a difference in the virulence genetic content between the clinical isolates causing an invasive infection and a colonizing clinical isolate nor between isolates from the clinical and environmental origin. The four novel A. fumigatus sequences had a different TRESP genotype and a total number of genetic variants ranging from 48,590 to 68,352. In addition, a comparative genomics analysis showed the presence of single nucleotide polymorphisms in VRGs and repetitive genetic elements located next to VRG groups, which could influence the regulation of these genes. In conclusion, our genomic analysis revealed a high genetic diversity between environmental and clinical A. fumigatus isolates, as well as between clinical isolates from the same patient, indicating an infection with a mixed-population in the latter case. However, all isolates had a similar virulence genetic content, demonstrating their pathogenic potential at least at the genomic level.

[Infectious keratitis in contact lens wearers]

Infectious keratitis in contact lens wearers Infectious keratitis is a sight-threatening complication in contact lens wearers. The infection is most frequently caused by bacteria (Pseudomonas aeruginosa). However, fungi or Acanthamoeba are found in increasing frequency. Three cases illustrate a characteristic course: patient A (11-year-old male) was treated for three weeks before the characteristic aspect of Acanthamoeba keratitis was recognized and confirmed. Patient B (45-year-old female) developed a severe corneal ulcer within 4 days; microbiological diagnostics confirmed Pseudomonas aeruginosa keratitis. Examination of patient C (27-year-old female) showed an infiltrate with satellites, typical of fungal keratitis. It is important to check the use of contact lenses in patients with keratitis. Referral to the ophthalmologist is mandatory: immediate in cases with an infiltrate. A dentritiform epithelial lesion in a contact lens wearer is indicative of Acanthamoeba keratitis, whereas fungal keratitis shows satellites or feathering edges. Steroids may only be prescribed by an ophthalmologist after confirmation of the causative agent.