Application of digital PCR to determine the reliability of Xpert Xpress SARS-CoV-2 assay with envelope (E) gene negative and nucleocapsid (N2) gene positive results.

This study used digital polymerase chain reaction (dPCR) to determine whether envelope (E) gene-negative and nucleocapsid (N2) gene-positive (E-N+) results obtained with the Cepheid Xpert Xpress SARS-CoV-2 assay are reliable. Using droplet digital PCR results as a reference, 18 of 22 E-N+ samples with a low viral load (81.8%) were identified as true positives.

Comparison of PneumID real-time PCR assay with Amplex eazyplex LAMP assay for laboratory diagnosis of Pneumocystis jirovecii Pneumonia.

We compared PneumID PCR with Amplex eazyplex LAMP assay for the diagnosis of Pneumocystis jirovecii pneumonia (PJP). Both assays enable accurate diagnosis of definite PJP. Cut-off cycle threshold of the PneumID assay was < 26.68 while the cut-off time-to-positivity of the eazyplex assay was 16:02 (minutes:seconds). The positive and negative percentage agreement of eazyplex assay with PneumID assay was 75.0% and 100.0% respectively, while the overall agreement was substantial with kappa = 0.80. For both assays, establishment of cut-off values to differentiate probable PJP from colonization was not feasible as results overlapped.

Both PneumID PCR and Amplex eazyplex LAMP assay enable accurate diagnosis of definite Pneumocystis jirovecii pneumonia (PJP). PneumID assay was more sensitive than eazyplex assay for detection of P. jirovecii. However, differentiation between probable PJP from colonization was not feasible.

An In Vitro Pilot Study on the Effects of Silver Diamine Fluoride on Periodontal Pathogens and Three-Dimensional Scaffolds of Human Fibroblasts and Epithelial Cells.

Objective: The aims of this study were to investigate the antibacterial and cytotoxic effects of silver diamine fluoride (SDF) on periodontal pathogens and human skin constructs, respectively. Background: SDF has been proven to have bactericidal effects on cariogenic bacteria. No studies to date evaluated the bactericidal effects of SDF on periodontal pathogens nor its effect on epithelium and fibroblasts. Methods: Streptococcus mutans, Porphyromonas gingivalis, and Aggregatibacter actinomycetemcomitans were cultured in monospecies biofilms, exposed to increasing concentrations of SDF and inoculated on agar plates to assess viability. Human gingival fibroblasts in 2D cultures were exposed to 1 µL of 0.394% of SDF and viewed using real-time imaging. Finally, SDF was applied to human, 3D tissue scaffolds of fibroblasts and keratinocytes, and termed human skin equivalents (HSE). A clinical dose of 38% SDF was applied, and HSE were cultured for 12 hours, 1, 3, 5, and 10 days. The tissue was observed clinically and histologically with hematoxylin and eosin staining and TUNEL. Results: S. mutans and A. actinomycetemcomitans growth was completely inhibited using all dilutions of SDF, whereas P. gingivalis was still viable with 0.197% and 0.098% of SDF. Single-layer fibroblasts experienced immediate necrosis upon contact with SDF. Application of SDF to HSE showed maturation of a whitish lesion within 24 hours, followed by pigmented, crusted tissue after 3 days. Histological evaluation of treated tissues showed apoptotic cells in the epithelium and upper half of the connective tissue. Conclusion: Our data suggest that SDF has bactericidal properties against two periodontal pathogens: P. gingivalis and A. actinomycetemcomitans. SDF caused immediate necrosis of monolayer fibroblasts, but does not extend to the full extent of layered fibroblasts in HSE.

Rapid adaptation and continuous performance evaluation of SARS-CoV-2 envelope gene (E-gene) real-time RT-PCR assays to support the hospital surge in test demand.

We describe the timely adaption of both published WHO E-gene protocol and commercially available LightMix Modular E-gene assay to the test platform (ABI 7900 Fast real-time analyzer and TaqMan Fast One-step Virus Master Mix) available in an accredited tertiary hospital laboratory with an on-going evaluation to ensure the provision of quality service within the time constraint. The LightMix Modular E-gene was slightly more sensitive when compared to the WHO E-gene, both analytically and diagnostically. The assay was recommended for screening of SARS-CoV-2 infection. With the availability of technically competent staff through continuous training, the provision of round-the-clock service is feasible despite the test is of high complexity. The thermal cycling duration of the adapted LightMix E-gene and WHO E-gene is shortened by half and one hour respectively and allows the number of runs to double when 24-h round-the-clock service is provided. An increase in testing capacity could support surges in testing demand, which is essential to control the current SARS-CoV-2 pandemic, to prevent potential overwhelming of the healthcare system, and to optimize utilization of the isolation beds.

Evaluation on testing of deep throat saliva and lower respiratory tract specimens with Xpert Xpress SARS-CoV-2 assay.

BACKGROUND: Xpert® Xpress SARS-CoV-2 assay is only validated on nasopharyngeal specimens for detection of SARS-CoV-2. Other specimen types such as deep throat saliva (DTS), also known as posterior oropharyngeal saliva and lower-respiratorytract specimens (LRT) including sputum, tracheal aspirate and bronchoalveolar lavage are not validated. These non-validated specimen types, however, do have significant diagnostic value. OBJECTIVE: Evaluate the performance of Xpert Xpress SARS-CoV-2 assay for detection of SARS-CoV-2 from DTS and LRT specimens. METHODS: 162 specimens from 158 patients with suspected COVID-19 disease were tested with Xpert Xpress SARS-CoV-2 assay. These included 120 DTS and 42 LRT specimens i.e. 35 sputum, 6 tracheal aspirate and one bronchoalveolar lavage. Results were compared to those by the TIB-Molbiol LightMix® SarbecoV E-gene assay. RESULTS: Xpert Xpress SARS-CoV-2 assay has satisfactory performance when compared with reference method. The positive percent agreement (PPA) of DTS and LRT specimens were 98.86 % & 100 % respectively while the negative percent agreement (NPA) was 100 % for both DTS and LRT specimens. CONCLUSIONS: This study demonstrated with appropriate sample pre-treatment, Xpert Xpress SARS-CoV-2 assay can be used to test on non-validated specimen types including DTS & LRT specimens.

Comparison of CaptiaTM Measles IgG Assay with Vidas® Measles IgG Assay for determination of immune protection status against measles virus.

BACKGROUND: Correlation of the assay cut-off values for CaptiaTM Measles IgG and the Vidas® Measles IgG assays with the World Health Organization recommended immunoprotective level of ≥120 mIU/mL is not stated by the manufacturers. Lack of such information may affect interpretation of immune protection (IP) for measles. OBJECTIVE: The aim of this study was to compare the relative performance of the CaptiaTM Measles IgG assay and the Vidas® Measles IgG assay for determination of IP against measles virus. STUDY DESIGN: Correlation of the cut-off value of both assays with the immunoprotective level was determined with the 3rd WHO Measles IgG International Standard. One hundred clinical samples including frozen and fresh were tested with both assays. The positive percentage agreement (PPA) based on the manufacturers' interpretation and the WHO recommended immunoprotective level was compared. RESULTS: Samples tested positive by the CaptiaTM assay were at or above the immunoprotective level while those tested equivocal and positive by the Vidas® assay were immune protective. The overall PPA between both assays was 78.31 % (95 % CI = 67.91-86.61%). When Vidas® equivocal results were regarded as immunoprotective, the overall IP agreement was 96.39 % (95 % CI = 89.80-99.25 %). CONCLUSIONS: CaptiaTM assay was more sensitive than the Vidas® assay in determination of IP against measles virus. Testing of measles immunity with the Vidas® Measles IgG assay might underestimate the IP unless equivocal results were regarded as immunoprotective.

Performance evaluation of the re-standardized Abbott Architect anti-HBs assay.

BACKGROUND: As defined by World Health Organization (WHO), an antibody level of ≥ 10mIU/mL to hepatitis B virus confers protection. With the launching of Abbott anti-HBs assay re-standardized to the 2nd WHO International Reference Preparation, a positive bias in antibody level would be anticipated. Manufacturer provides limited data for samples around the immune cut-off which has potential implication on vaccine guidance. OBJECTIVES: To evaluate the performance of the re-standardized Abbott Architect anti-HBs assay and to determine the impact of the upward shift. STUDY DESIGN: A total of 52 samples, including 12 external quality assurance programme samples and 40 clinical samples were tested with both the Abbott 1st WHO standardized and the 2nd WHO re-standardized assay and results compared. The 2nd WHO anti-HBs standard and Acometrix anti-HBs control were also included for comparison. RESULTS: Verification of the re-standardized assay with the 2nd WHO anti-HBs standard revealed positive bias with mean closer to target value. Overall, the positive bias introduced by the new assay will only affect interpretation of samples with anti-HBs levels > 5.00 to < 10.00 mIU/mL previously tested on the Abbott 1st WHO standardized anti-HBs assay. CONCLUSIONS: Final interpretation of immune status to hepatitis B was not affected by the upward shift following introduction of the new Abbott anti-HBs assay except for previously negative samples with anti-HBs levels between >5.00 to <10.00 mIU/mL.

Comparison of the Cepheid Xpert Xpress Flu/RSV Assay to in-house Flu/RSV triplex real-time RT-PCR for rapid molecular detection of Influenza A, Influenza B and Respiratory Syncytial Virus in respiratory specimens.

This study compared the performance of the commercially available Xpert Xpress Flu/RSV assay to an in-house FluAB/RSV triplex real-time RT-PCR assay for the detection of influenza A/B viruses and respiratory syncitial virus (RSV) from both nasopharyngeal aspirate (NPA) and nasopharyngeal flocked swab (NPS). A total of 20 external quality assurance (EQA) samples and 172 clinical respiratory samples were tested prospectively using both the Xpert Xpress Flu/RSV assay and the in-house FluAB/RSV triplex assay. For the EQA samples, concordance rate was 100 % when tested with both assays. For clinical samples, there was 100 % agreement between the two assays for detection of influenza A and influenza B, 96.7 % agreement for detection of RSV and 99.7 % agreement for negative results. With a shortened turnaround time and good diagnostic performance, application of the Xpert Xpress Flu/RSV assay can facilitate patient triage for prompt implementation of infection control measures and management of high-risk patients during influenza epidemics.

Surveillance of antibiotic resistance among common Clostridium difficile ribotypes in Hong Kong.

Incidence of Clostridium difficile infection (CDI) is rapidly increasing and it poses a major health burden globally. However, data regarding the epidemiology of CDI in Asia are limited. We aimed to characterize the antimicrobial susceptibility patterns of common ribotypes of toxigenic C. difficile in Hong Kong. Fifty-three PCR ribotypes were identified among 284 toxigenic C. difficile clinical isolates. The five most prevalent ribotypes were 002 (13%), 017 (12%), 014 (10%), 012 (9.2%), and 020 (9.5%). All tested C. difficile strains remained susceptible to metronidazole, vancomycin, meropenem and piperacillin/tazobactam, but highly resistant to cephalosporins. Of the fluoroquinolones, highest resistance to ciprofloxacin was observed (99%), followed by levofloxacin (43%) and moxifloxacin (23%). The two newly emerged PCR ribotypes, 017 and 002, demonstrated high levels of co-resistance towards clindamycin, tetracycline, erythromycin and moxifloxacin. PCR ribotypes 017 and 002 with multi-drug resistance are rapidly emerging and continuous surveillance is important to monitor the epidemiology of C. difficile to prevent outbreaks of CDI.

Development and comparison of molecular assays for the rapid detection of the pandemic influenza A (H1N1) 2009 virus.

Human infection with the novel pandemic influenza A (H1N1) virus was first identified in April 2009. Two months later, the World Health Organization (WHO) had raised the pandemic level to phase 6. Rapid case identification is essential for prompt patient management and public health actions. This study developed real-time and conventional reverse transcription-polymerase chain reaction (rRT-PCR and cRT-PCR) assays for pandemic H1N1 detection, and compared their sensitivities with protocols developed by WHO reference centres. Altogether, three rRT-PCR and one cRT-PCR targeting the matrix gene for universal detection of influenza A; three rRT-PCR, one cRT-PCR targeting the hemagglutinin (HA) gene for specific detection of pandemic H1N1; and one multiplex cRT-PCR for differentiating co-circulating seasonal H1N1, H3N2, and pandemic H1N1 were examined. The lower detection limit ranged from 1.252 to 125.2 copy equivalents. In general, rRT-PCR assays were more sensitive than cRT-PCR assays. All assays showed 100% sensitivity for "optimal" specimens (nasopharyngeal samples collected within 4 days after illness onset). For the other 36 samples, cRT-PCR assays were less sensitive except that the new Protocol I-cRT-pdmH1 still retained 100% sensitivity. The new Protocol F-rRT-PCR-pdmH1 was the only pandemic virus-specific rRT-PCR assay with 100% sensitivity across all specimen categories. In conclusion, rRT-PCR assays are 10-fold more sensitive than cRT-PCR assays. The newly developed cRT-PCR assay targeting the HA gene allows rapid, specific, and sensitive screening of this novel agent, which can serve as an alternative for laboratories where a real-time PCR machine is not available.