Analytical evaluation and critical appraisal of early commercial SARS-CoV-2 immunoassays for routine use in a diagnostic laboratory.

Background: The objective of this study was to evaluate the performance characteristics of early commercial SARS-CoV-2 antibody assays in mild and asymptomatic subjects to enable the selection of suitable immunoassays for routine diagnostic use.Methods: We used serum samples from a pre-COVID era patient cohort (n = 50, pre-December 2019), designated SARS-CoV-2 negative, and serum samples from a SARS-CoV-2 RT-PCR-positive cohort (n = 90) taken > 14 days post-symptom onset (April-May 2020). Six ELISA assays were evaluated, including one confirmation assay to investigate antibody specificity. We also evaluated one point-of-care lateral flow device (LFIA) and one high throughput electrochemiluminescence immunoassay (CLIA).Results: The ELISA specificities ranged from 84% to 100%, with sensitivities ranging from 75.3% to 90.0%. The LFIA showed 100% specificity and 80% sensitivity using smaller sample numbers. The Roche CLIA immunoassay showed 100% specificity and 90.7% sensitivity. When used in conjunction, the Euroimmun nucleocapsid (NC) and spike-1 (S1) IgG ELISA assays had a sensitivity of 95.6%. The confirmation Dia.Pro IgG assay showed 92.6% of samples tested contained both NC and S1 antibodies, 32.7% had NC, S1 and S2 and 0% had either S1 or S2 only.Conclusions: The Roche assay and the Euroimmun NC and S1 assays had the best sensitivity overall. Combining the assays detecting NC and S1/S2 antibody increased diagnostic yield. These first-generation assays were not calibrated against reference material and the results were reported qualitatively. A portfolio of next-generation SARS-CoV-2 immunoassays will be necessary to investigate herd and vaccine-induced immunity.

The Unyvero P55 'sample-in, answer-out' pneumonia assay: A performance evaluation.

BACKGROUND: O'Neill's recent Review on Antimicrobial Resistance expressed the view that by 2020 high-income countries should make it mandatory to support antimicrobial prescribing with rapid diagnostic evidence whenever possible. METHODS: Routine microbiology diagnosis of 95 respiratory specimens from patients with severe infection were compared with those generated by the Unyvero P55 test, which detects 20 pathogens and 19 antimicrobial resistance markers. Supplementary molecular testing for antimicrobial resistance genes, comprehensive culture methodology and 16S rRNA sequencing were performed. RESULTS: Unyvero P55 produced 85 valid results, 67% of which were concordant with those from the routine laboratory. Unyvero P55 identified more potential pathogens per specimen than routine culture (1.34 vs. 0.47 per specimen). Independent verification using 16S rRNA sequencing and culture (n = 10) corroborated 58% of additional detections compared to routine microbiology. Overall the average sensitivity for organism detection by Unyvero P55 was 88.8% and specificity was 94.9%. While Unyvero P55 detected more antimicrobial resistance markers than routine culture, some instances of phenotypic resistance were missed. CONCLUSIONS: The Unyvero P55 is a rapid pathogen detection test for lower respiratory specimens, which identifies a larger number of pathogens than routine microbiology. The clinical significance of these additional organisms is yet to be determined. Further studies are required to determine the effect of the test in practise on antimicrobial prescribing and patient outcomes.

'Sample-in, answer-out'? Evaluation and comprehensive analysis of the Unyvero P50 pneumonia assay.

This study aimed to evaluate the performance of the Unyvero P50 pneumonia assay, the first 'sample-in, answer-out' system for rapid identification of pathogens and antibiotic resistance markers directly from clinical specimens. Overall, Unyvero P50 displayed very good sensitivity (>95%); however, specificity was low (33%) mainly because 40% of the specimens were reported as normal flora. Specifically, one or more pathogens were identified in 28 of them. From a detailed analysis of 42 specimens selected at random, 76% of the additionally reported pathogens were confirmed present in primary specimens. Detection of selected resistance markers was compared to routine phenotypic susceptibility testing, supplemented with Checkpoints microarray system, PCR and sequencing. Concordance was mixed, primarily due to issues with panel's choice of markers and detection of some intrinsic beta-lactamases. Finally, we offer a critical analysis of the assay's microbial panel and resistance markers and provide suggestions for improvement.

The management of periprosthetic infections in the future: a review of new forms of treatment.

The number of arthroplasties being undertaken is expected to grow year on year, and periprosthetic joint infections will be an increasing socioeconomic burden. The challenge to prevent and eradicate these infections has resulted in the emergence of several new strategies, which are discussed in this review. Cite this article: Bone Joint J 2015;97-B:1162-9.

Influenza virus survival in aerosols and estimates of viable virus loss resulting from aerosolization and air-sampling.

Using a Collison nebulizer, aerosols of influenza (A/Udorn/307/72 H3N2) were generated within a controlled experimental chamber, from known starting virus concentrations. Air samples collected after variable suspension times were tested quantitatively using both plaque and polymerase chain reaction assays, to compare the proportion of viable virus against the amount of detectable viral RNA. These experiments showed that whereas influenza RNA copies were well preserved, the number of viable viruses decreased by a factor of 10(4)-10(5). This suggests that air-sampling studies for assessing infection control risks that detect only influenza RNA may greatly overestimate the amount of viable virus available to cause infection.

Performance of ultramicrofibre cleaning technology with or without addition of a novel copper-based biocide.

This study compared the bacterial removal performance of ultramicrofibre cloths and mops (UMF) moistened with water (UMF+water), with those moistened with a novel copper-based biocide (UMF+CuWB50, 300ppm) in several working hospital environments, specifically accident and emergency (A&E) and three other wards. A total of 13 defined sampling sites (10 sites per ward) were sampled in order to retrieve, culture, and enumerate total viable (bacterial) counts (TVC) for each site. We sampled 1h before, and 1 and 4h after, cleaning three times per week. The trial ran for 7 weeks. Two wards were cleaned with UMF+water for 3 weeks, and UMF+CuWB50 for 4 weeks. The reverse applied to the other two wards in a cross-over design fashion, to eliminate ward- and time-specific bias. Multivariate statistical analyses were used to establish extent and significance of any perceived differences, and to eliminate the effects of potential confounders. Cleaning with UMF+water reduced TVC on the test surfaces by 30%, whereas cleaning with TVC+CuWB50 reduced TVC by 56%. CuWB50 had two separate effects; a direct antibacterial effect (evident shortly after cleaning), and a residual antibacterial effect that lasted approximately 2 weeks. The residual effect requires regular application of CuWB50 if it is to persist. This 'real life' hospital implementation study demonstrates encouraging microbiological cleaning performance for UMF, which is further enhanced with CuWB50.

Multiplex real-time PCR and blood culture for identification of bloodstream pathogens in patients with suspected sepsis.

Severe sepsis is increasingly a cause of death. Rapid and correct initial antimicrobial treatment reduces mortality. The aetiological agent(s) cannot always be found in blood cultures (BCs). A novel multiplex PCR test (SeptiFast (alpha version)) that allows identification of 20 bacterial and fungal species directly from blood was used, comparatively with BC, in a multicentre trial of patients with suspected bacterial or fungal sepsis. Five hundred and fifty-eight paired samples from 359 patients were evaluated. The rate of positivity was 17% for BC and 26% for SeptiFast. Ninety-six microorganisms were isolated with BC, and 186 microorganisms were identified with SeptiFast; 231 microorganisms were found by combining the two tests. Of the 96 isolates identified with BC, 22 isolates were considered to be contaminants. Of the remaining 74 non-contaminant BC isolates available for comparison with SeptiFast, 50 were identified as a species identical to the species identified with SeptiFast in the paired sample. Of the remaining 24 BC isolates for which the species, identified in the BC, could not be detected in the paired SeptiFast sample, 18 BC isolates were identified as a species included in the SeptiFast master list, and six BC isolates were identified as a species not included in the SeptiFast master list. With SeptiFast, 186 microorganisms were identified, 12 of which were considered to be contaminants. Of the 174 clinically relevant microorganisms identified with SeptiFast, 50 (29%) were detected by BC. More than half of the remaining microorganisms identified with SeptiFast (but not isolated after BC) were also found in routine cultures of other relevant samples taken from the patients. Future clinical studies should assess whether the use of SeptiFast is of significant advantage in the detection of bloodstream pathogens.

Removing bacteria from hospital surfaces: a laboratory comparison of ultramicrofibre and standard cloths.

We compared the ability of ultramicrofibre-woven cloths with conventional cloths moistened with water only, for their ability to remove several types of organisms relevant to hospital-acquired infections from a variety of surfaces in hospitals. We showed that ultramicrofibre cloths consistently outperformed conventional cloths in their decontamination ability, across all surfaces, and irrespective of whether the bacteria were coated on to the surfaces with phosphate-buffered saline (PBS) or PBS containing horse serum to simulate real-life soiling. The ability of the cloths to remove bacteria from surfaces was assessed by contact plating and colony formation, and by swabbing and measurement of ATP bioluminescence. The results suggest potential for use of ultramicrofibre in healthcare environments. Further studies are required, however, to define accurately how these cloths, which are designed to be used without detergent or biocides, might be capable of safe and effective deployment and recycling in the healthcare environment.

The efficacy of the inorganic copper-based biocide CuWB50 is compromised by hard water.

AIMS: We sought to explain the unexpected failure of the inorganic copper-based biocide CuWB50 to effectively decontaminate microfibre cleaning cloths that became contaminated with Acinetobacter lwoffii. METHODS AND RESULTS: CuWB50 was diluted using distilled water or tap water obtained from two different ICUs. Microtitre plate assays were used to determine the minimum inhibitory concentration (MIC) for the implicated A. lwoffii. pH and oxidation-reduction potential (ORP) tests were performed and representative water samples were chemically analysed. When diluted in distilled water, the CuWB50 MIC for A. lwoffii was 9 mg l(-1) but in tap water from each ICU it was 37 and 75 mg l(-1) at hardness levels of 246 and 296 mg CaCO(3) l(-1) respectively. CuWB50-distilled water solutions consistently had a lower pH and higher ORP than CuWB50-tap water solutions. CONCLUSIONS: Hard water adversely affects the biocidal efficacy of CuWB50. SIGNIFICANCE AND IMPACT OF THE STUDY: Unintentional environmental contamination is a risk when using wet microfibre cloths. This occurred when cloths were stored in CuWB50 overnight combined with the unintentional but erroneous use of tap water. This study emphasizes the need for clearly documented cleaning protocols embedded within a culture of adequate training and constant supervision of cleaning staff.

Development and evaluation of a real-time PCR assay for detection of Pneumocystis jirovecii DNA in bronchoalveolar lavage fluid of HIV-infected patients.

BACKGROUND: Pneumocystis pneumonia (PCP) is conventionally diagnosed by identifying Pneumocystis jirovecii in lower respiratory tract samples using cytochemical stains. Molecular diagnosis of PCP is potentially more sensitive. METHODS: A study was undertaken to use an extensively optimised real-time polymerase chain reaction (PCR) using primers designed to hybridise with the P. jirovecii heat shock protein 70 (HSP70) gene to quantify P. jirovecii DNA in bronchoalveolar lavage (BAL) fluid from HIV-infected patients with and without PCP, and to compare this assay with conventional PCR targeting the P. jirovecii mitochondrial large subunit rRNA gene sequence (mt LSU rRNA). RESULTS: Sixty-one patients had 62 episodes of PCP (defined by detection of P. jirovecii in BAL fluid by cytochemical stains and typical clinical presentation). Quantifiable HSP70 DNA was detected in 61/62 (range approximately 13-18,608 copies/reaction; median approximately 332) and was detectable but below the limit of quantification (approximately 5 copies/reaction) in 1/62. Seventy-one other patients had 74 episodes with alternative diagnoses. Quantifiable HSP70 DNA was detectable in 6/74 (8%) episodes (range approximately 6-590 copies/reaction; median approximately 14) and detectable but below the limit of quantification in 34/74 (46%). Receiver-operator curve analysis (cut-off >10 copies/reaction) showed a clinical sensitivity of 98% (95% 91% to 100%) and specificity of 96% (95% CI 87% to 99%) for diagnosis of PCP. By contrast, clinical sensitivity of mt LSU rRNA PCR was 97% (95% CI 89% to 99%) and specificity was 68% (95% CI 56% to 78%). CONCLUSION: The HSP70 real-time PCR assay detects P. jirovecii DNA in BAL fluid and may have a diagnostic application. Quantification of P. jirovecii DNA by real-time PCR may also discriminate between colonisation with P. jirovecii and infection.

Use of surface-enhanced Raman spectroscopy for the detection of human integrins.

Current research has revealed the importance of a class of cell surface proteins called integrins in various vital physiological functions such as blood clotting, regulation of blood pressure, tissue blood flow, and vascular remodeling. The key to integrin functionality is its ability to mediate force transmission by interacting with the extracellular matrix and cytoskeleton. In addition, they play a role in signal transduction via their connection with the proteins in focal adhesion (FA) points. To understand the complex mechanism of cell-cell and cell-extracellular matrix (ECM) adhesion that is responsible for these diverse biochemical interactions, it is necessary to identify the integrins on cells and monitor their interaction with various ligands. To this end, for the first time, we employ surface-enhanced Raman spectroscopy (SERS) to detect integrins. The results show the capability using SERS to detect the integrins to the nanomolar concentration regime and to distinguish between two different kinds of integrins, alphaVbeta3 and alpha5beta1, that are present in vascular smooth muscle cells (VSMCs). It is anticipated that the SERS approach will potentially help elucidate the mechanism of integrin-ligand interactions in a variety of phenomena of physiological importance.

Mitochondrial K(ATP) channel opening protects a human atrial-derived cell line by a mechanism involving free radical generation.

OBJECTIVES: The mechanism by which the mitochondrial K(ATP) channel openers confer protection against ischemia/reperfusion injury is debated. Evidence suggests that rather than solely being an end effector, opening of these channels may act by a trigger mechanism. We examined the effects of the mitochondrial K(ATP) channel opener, diazoxide on parameters of mitochondrial function with specific reference to reactive oxygen species (ROS) generation in a human atrial derived cell line model of simulated ischemia/reperfusion (LSI/R). METHODS AND RESULTS: Propidium iodide (PI) exclusion was used to assess survival. Diazoxide treatment conferred protection against LSI/R (13.9+/-0.9% vs. 36.9+/-4.5% controls) that was abolished by pre-treatment with the mitoK(ATP) channel blocker, 5-hydroxydecanoate (5-HD) (33.3+/-3.6%) and with the free radical scavenger, 2-mercaptopropionylglycine (MPG) (29+/-4.0%). Diazoxide caused increased oxidation of the ROS probe, reduced mitotracker orange (1.3 vs. 1.0 arbitrary units for control; P<0.01 vs. control) that was abrogated by either 5-HD or MPG (1.07 and 1.07 arbitrary units, respectively). At the same time there was no change in orange fluorescent signal from the membrane potential sensitive probe, JC-1 indicating no change in mitochondrial membrane potential. Changes in light scattering, reflecting changes in mitochondrial volume, occurred during treatment with diazoxide. CONCLUSION: These results demonstrate for the first time that the mitoK(ATP) channel opener diazoxide can act as a trigger of preconditioning by a mechanism involving mitochondrial swelling and the generation of ROS.

Increased distribution and expression of CD64 on blood polymorphonuclear cells from patients with the systemic inflammatory response syndrome (SIRS).

Evidence is growing to suggest that the multiple organ damage of the systemic inflammatory response syndrome (SIRS) arises from the untoward activity of blood polymorphonuclear cells (PMNs), which upon activation acquire the IgG high affinity receptor, CD64. In the current study, flow cytometry was used to assess the prevalence of CD64-bearing PMNs and the intensity of expression of CD64 in whole blood samples from 32 SIRS patients, 11 healthy normal subjects and from eight non-SIRS patients in the intensive care unit (ICU). The percentage of PMNs expressing CD64 was higher in SIRS patients (mean 65%) than in non-SIRS patients (mean 42%; P < 0.02) and in healthy controls (mean 19%; P < 0.001) and was particularly evident in patients with SIRS and sepsis (mean 71%; P < 0.02) as opposed to SIRS alone (mean 55%). There were more CD64 molecules expressed on PMNs from patients with SIRS (median 1331 molecules/cell) in comparison with PMNs from healthy subjects (median 678 molecules/cell; P < 0.01). The highest intensity of CD64 expression was associated with PMNs from patients with both SIRS and sepsis. Functional studies revealed that the supranormal binding of PMNs from patients with SIRS to endothelial monolayers treated with TNFalpha was impeded by anti-CD64 antibodies (mean 24% inhibition; P < 0.01). Monitoring the distribution of CD64+ PMNs and their level of CD64 expression could be of assistance in the rapid discrimination of patients with SIRS from other ICU patients and in the identification of PMNs which are likely to participate in the pathological manifestations of the disease.

The effects of leucodepletion in patients who develop the systemic inflammatory response syndrome following cardiopulmonary bypass.

The development of the systemic inflammatory response syndrome (SIRS) is associated with increased morbidity and mortality. Numerous anticytokine trials have failed to demonstrate any outcome benefit and there has been little evidence of improvement in the prognosis of this condition over the past 20 years. This study examines the effect of using a white cell filter designed to remove polymorphonuclear cells (PMNs) in patients who developed SIRS 36 h after cardiopulmonary bypass (CPB). Twenty-four patients were randomized to receive either leucofiltration (LF) or control therapy (CT). The two groups were well matched at study entry in terms of age, severity of illness and length of time on CPB. LF patients received 60 min filtration periods using a venovenous extracorporeal circuit at a flow rate of 200 ml/min with the cycle repeated every 12 h while SIRS and other entry criteria were met. CT patients received standard therapy. LF patients received an average of 4.2 cycles (range 1-8) and, after 15 min filtration, the total leucocyte count had fallen from 16.2 +/- 5.3 to 10.4 +/- 3.3 x 10(9)/l and PMN from 14.4 +/- 5.2 to 8.3 +/- 4.2 x 10(9)/l. The mean platelet count changed from 127 +/- 87 to 117 +/- 82 x 10(9)/l. No adverse effects related to leucodepletion were observed. There was no difference between the groups in either mortality or length of stay at the intensive care unit or at hospital discharge. Organ function was assessed regularly during the study period and significant changes occurred only in respiratory and renal function. In the LF patients, respiratory function assessed by change in hypoxaemia index from baseline and renal function assessed by serum creatinine showed significant treatment effects compared to CT patients (p < 0.01, < 0.01 respectively); three CT patients, but no LF patients, received haemofiltration during the study period. Leucofiltration safely and effectively removes circulating PMNs from patients with SIRS following CPB. This may result in improved pulmonary and renal function in these patients. Further studies are required of the kinetics and phenotypic characteristics of PMN removal by leucofiltration and a larger multicentre study will be necessary to determine whether this novel therapy has a significant outcome benefit in critically ill patients with SIRS.

Antibiotic susceptibility testing by flow cytometry.

Flow cytometry can provide a rapid indication of antibiotic susceptibility. This unit describes a number of fluorescent dyes that allow the cytometer to distinguish the heterogeneic nature of populations exposed to antibiotics. No single method can be used for multiple organisms, since it is the interference with the organisms growth and structural integrity that signals the impact of the antibiotic so rapidly. This unit discusses membrane structural changes as well as alterations in nucleic acid and the probes that can be successfully used with flow cytometry.