Breakthrough Invasive Fungal Infections in Patients With High-Risk Hematological Disorders Receiving Voriconazole and Posaconazole Prophylaxis: A Systematic Review.

BACKGROUND: Primary antifungal prophylaxis with mold-active azoles is used to prevent invasive fungal infections in patients with high-risk hematological disorders; however, breakthrough infections occur, and the reasons for treatment failure are still not fully understood. To help inform clinical decisions, we sought to define microbiological, clinical, and pharmacological characteristics of proven and probable breakthrough invasive fungal infections (bIFIs) in patients with high-risk hematological disorders receiving voriconazole or posaconazole prophylaxis. METHODS: We performed a systematic review of the literature following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The search strategy was last conducted on 19 April 2023. RESULTS: We assessed 5293 studies for eligibility, and 300 were selected for data extraction. These studies described 1076 cases of bIFIs occurring under voriconazole (42.5%) or posaconazole (57.5%). The most commonly found pathogens were Aspergillus (40%), Mucorales (20%), Candida (18%), and Fusarium (9%) species. Mucorales were more frequent among voriconazole-emerging cases, whereas Aspergillus and Fusarium were more prevalent among posaconazole-emerging cases. Definitive, putative, or probable antifungal resistance was found in 31% of cases. Therapeutic drug monitoring showed subtherapeutic azole concentration in 32 of 90 (36%) cases. Infection-related mortality was reported in 117 cases and reached 35%. CONCLUSIONS: In our systemic review, the most common bIFIs were aspergillosis, mucormycosis, candidiasis, and fusariosis. Antifungal resistance explains only a minority of cases. Subtherapeutic prophylaxis was frequent but rarely reported. Prospective studies are needed to better understand these infections and to establish optimal management.

A new direction for cytomegalovirus prophylaxis among transplant recipients: Benefits and nonviral outcomes of letermovir use as primary CMV prophylaxis.

PURPOSE OF REVIEW: Letermovir has changed the game of primary prophylaxis against cytomegalovirus (CMV) for hematopoietic stem cell transplant (HSCT) and more recently, solid organ transplant recipients. This is largely due to letermovir's similar efficacy in protecting against CMV reactivation and disease, along with its superior safety profile, notably reduced myelotoxicity, and lack of renal dose adjustment compared to standard agents like valganciclovir. This review will describe the potential benefits and clinical considerations of letermovir as prophylaxis among transplant recipients, with a focus on recent evidence describing nonviral outcomes of CMV. RECENT FINDINGS: Recent evidence has demonstrated improved safety (e.g., less myelosuppression) and tolerability with no difference in rates of CMV infection or disease in kidney transplant recipients given letermovir compared to valganciclovir. Real-world studies and meta-analyses in HSCT populations have explored various nonviral outcomes with letermovir use. Letermovir prophylaxis was associated with reduced mortality, lower rates of graft versus host disease, delayed CMV immune reconstitution, improved tolerability with extended durations, and decreased healthcare utilization. SUMMARY: Letermovir is an effective antiviral agent for CMV prevention and has demonstrated enhanced safety, which may allow for extended durations of primary prophylaxis among transplant recipients along with other improved clinical outcomes by mitigating the indirect effects of CMV.

Systematic fungal biomarker or polymerase chain reaction testing in lung transplant recipients: Retrospective analysis to optimize their use.

BACKGROUND: Among lung transplant recipients, serial bronchoscopies are performed frequently. Often, serial galactomannan (GM), 1,3-ß-d-glucan (BDG), and Pneumocystis jirovecii (PJ) testing is performed with these broncho-alveolar lavages (BALs) as standard of care with limited data to support their routine use. METHODS: After Institutional Review Board approval, we retrospectively collected all blood and BAL GM, BDG, and PJ test results from January 2015 to July 20, 2022. Primary data collection from the Northwestern Medicine EDW was supplemented by manual chart review. RESULTS: During the study period, 236 lung transplant recipients were cared for by our center. Of these patients, 217 (91.9%) had 1418 GM tests performed; 61 (4.3%) were positive (index ≥1). Fungal cultures were requested for most BAL-GM (90.7%). Out of duplicates in same BAL, results discrepancy was minimal (3.4%). 172 (72.9%) had BDG tests were performed; 25.6% were positive. Thirteen patients had multiple BDG during one hospitalization (mean 2.3 tests); none of the negative test repeated became positive. Eleven negative BDG were seen in patients with invasive aspergillosis (IA). Note that, 577 PJ testing were performed (direct fluorescent antibody [n = 494] or polymerase chain reaction [PCR] [n = 80], or both [n = 3]) in 174 different patients. None were positive. CONCLUSION: Despite supplemental GM, BDG, and Pneumocystis jirovecii pneumonia PCR being performed routinely on lung transplant recipients undergoing BAL at our center, the data suggests a more tailored approach may be appropriate. There is no role for routine serial testing with these assays during a single hospitalization. BDG confers no added-value over GM with cultures for IA diagnosis.

Utility of deceased donor cultures in solid organ transplantation in preventing donor-derived bacterial and fungal infectious diseases transmission.

Deceased donor and organ perfusion fluid cultures are obtained in order to inform recipient antimicrobial management and therefore reduce the risk of donor-derived bacterial and fungal infections. However, important heterogeneity exists in laboratory practice across organ procurement organizations and clinical management of culture results across transplant centers. While not standardized, the clinical approach to donors with positive bacterial and/or fungal cultures should be informed by the risk of donor-derived infection (DDI) and the consequence of organ non-utilization and account for potential unintended effects of antimicrobial use in the recipient. In this review, we summarize the literature on bacterial and fungal DDIs, describe the significance of positive cultures by anatomic site, and summarize current guidance on the management of positive cultures from donors or preservation fluids.

Flow path monitoring by discontinuous time-lapse ERT: An application to survey relationships between secondary effluent infiltration and roots distribution.

The infiltration of secondary treated effluent (STE) into the soil downstream of wastewater treatment plants is becoming increasingly common in a climate change context. In STE infiltration, STE is discharged onto the soil over a large surface allowing for a gradual infiltration of the water. This paper investigates a novel time-lapse electrical resistivity tomography strategy to evaluate the impact of STE infiltration on the water pathways of two planted loamy-soil trenches located in a Fluvisol region in southwestern France. The system has been monitored for 3 years using discontinuous monitoring of electrical resistivity tomography during four saline tracer tests. Results show that: 1) the new methodology has successfully highlighted the evolution of water pathways in the soil over time; 2) such evolution is in agreement with reeds root distribution in the trenches which seems to be affected by water quality i.e. sludge losses and TSS, for this study case. Indeed, for the infiltration trench receiving STE with lower pollution levels (2.2 mg TSS. L-1, 26 mg COD. L-1), the infiltration capacity is maintained over the years (4-6 mm h-1) and reed roots developed deeper in the soil. A sludge deposit present at the bottom of the second infiltration trench receiving higher pollution levels (7.2 mg TSS. L-1, 45 mg COD. L-1, plus episodic sludge release) could lead roots to develop close to the surface affecting the infiltration capacity which did not evolve over time. This work highlights the importance of long-term flow pathway monitoring in understanding the hydraulic behavior of infiltration surfaces submitted to STE.

Update on Covid-19: vaccines, timing of transplant after COVID-19 infection and use of positive donors.

PURPOSE OF REVIEW: SARS-CoV-2 resulted in a global pandemic that had a chilling effect on transplantation early in the pandemic and continues to result in significant morbidity and mortality of transplant recipients. Over the past 2.5 years, our understanding of the clinical utility of vaccination and mAbs to prevent COVID-19 in solid organ transplant (SOT) recipients has been studied. Likewise, approach to donors and candidates with SARS-CoV-2 has been better understood. This review will attempt to summarize our current understanding of these important COVID-19 topics. RECENT FINDINGS: Vaccination against SARS-CoV-2 is effective in reducing the risk of severe disease and death among transplant patients. Unfortunately, humoral and, to a lesser extent, cellular immune response to existing COVID-19 vaccines is reduced in SOT recipients compared with healthy controls. Additional doses of vaccine are required to optimize protection of this population and still may be insufficient in those who are highly immunosuppressed, those receiving belatacept, rituximab and other B-cell active mAbs. Until recently, mAbs were options for the prevention of SARS-CoV-2 but are markedly less effective with recent omicron variants. SARS-CoV-2-infected donors can generally be used for nonlung, nonsmall bowel transplants unless they have died of acute severe COVID-19 or COVID-19-associated clotting disorders. SUMMARY: Our transplant recipients require a three-dose mRNA or adenovirus-vector and one dose of mRNA vaccine to be optimally protected initially; they then need to receive a bivalent booster 2+ months after completing their initial series. Most nonlung, nonsmall bowel donors with SARS-CoV-2 can be utilized as organ donors.

Quantification and qualification of the urban domestic pollution discharged per household and per resident.

The research study aims to analyze the discharges of solely domestic wastewater from 15 single-family dwellings. This sizable dataset, containing over 300 unique and insightful data points, makes it possible to accurately qualify the raw wastewater in terms of concentrations, volumes and pollutant loads. Findings quantify the extremely wide data variability. As such, for single-family households of fewer than six residents, it is suggested not to use the standard P.E. pollution value as the design load, but rather a load range defined by the interval [10th percentile, 90th percentile] of the data distribution, i.e. [123; 568 L·d- 1] and [30; 281 g BOD5·d-1], respectively, for the daily hydraulic and organic loads. Also, an analysis of the hydraulic peak factor would tend to lobby in favor of a collective sewer solution. For subdivisions and residential zones with little economic activity and similar French lifestyle, the daily domestic pollution per resident is now determined with the values: 40 g suspended solids, 94 g carbon oxygen demand, 40 g five-day biochemical oxygen demand, 6.7 g NH4+-N, 10.4 g Kjeldhal nitrogen, and 1.2 g total phosphorus for a volume of 83 L. Those data could be used to optimize design and operation of decentralized or small-scale wastewater treatment plant.

Prediction of household wastewater treatment systems' in situ performance based on standardized tests.

This paper presents a comparative analysis on operating conditions of onsite wastewater treatment systems. Actual EU Member States' national regulations require in situ treatment thresholds expressed in effluent concentrations. CE marking of onsite wastewater treatment system is mandatory according to standardized test (EN 12566-3 + A2) with performance declared in removal efficiency. Recent study indicates that in situ raw sewage concentrations are 1.5 times higher than those on test platforms. In this context, performance comparison between platform tests and in situ discharge threshold cannot be based on effluent concentrations but rather on removal efficiency to fulfill environmental and health requirements. This study compares: (i) results from eight standardized tests, (ii) over 300 measurements of in situ raw sewage, and (iii) several national-level thresholds focusing on carbon parameters. To meet French effluent thresholds, a minimum removal efficiency of 96% in SS and 95% in BOD5 is required. A beta law model assesses the efficiency measured during standardized testing and establishes a robustness characteristic with a probability above 80%. When a septic tank is used, its efficiency can be incorporated into the prediction. Although the new performance criteria are more stringent, some of the eight products evaluated still meet the requirements.

Risks of hepatitis C virus reactivation in a real-life population of oncology patients treated in an academic center.

BACKGROUND: Chemotherapy has been associated with a theoretical risk of hepatitis C virus (HCV) reactivation. However, little is known about the amplitude of viral replication and the incidence of subsequent hepatic exacerbation. METHOD: We aimed to describe the occurrence of hepatitis flare and HCV reactivation at our center. We included, over a period of 5 years, adult patients with chronic HCV receiving intravenous chemotherapy. We excluded patients with undetectable HCV RNA, hepatocellular carcinoma, liver metastases or other etiologies of hepatic disease. The primary objective was to identify hepatic flares (elevation of alanine aminotransferase 3 times above the upper limit of normal). Secondary objectives were to assess viral reactivation (HCVr, HCV-RNA ≥1 log10 IU/mL when compared to baseline value), hepatic decompensation, mortality and the impact on the chemotherapy. Descriptive statistics were used. RESULTS: A total of 11 patients with chronic HCV were identified among the 5761 oncology patients. Five patients experienced a hepatic flare with median maximal ALT value of 139 U/L (IQR 133-237). Only 2 patients met criteria for HCVr with a median RNA increase of 1.16 log IU/mL (IQR 1.1-1.2). One patient presented with both HCVr and a hepatic flare. Only one patient required chemotherapy discontinuation following hepatic flare. No hepatic decompensation or related mortality were observed. CONCLUSION: We identified a very small number of HCV cases among our population. We observed HCVr and hepatic flares, but only one consequence on cancer treatment. Nonetheless, HCV screening is encouraged among patients undergoing chemotherapy to allow close follow-up of hepatic function.

Fate of two strains of extended-spectrum beta-lactamase producing Escherichia coli in constructed wetland microcosm sediments: survival and change in antibiotic resistance profiles.

Free water surface constructed wetlands (FWS CW) are efficient technologies to limit the transfer of antibiotic resistant bacteria (ARB) originating from urban effluents into the aquatic environment. However, the decrease in ARB from inflow to outflow through the FWS CW may be explained by their transfer from the water body to the sediment. To investigate the behavior of ARB in the sediment of a FWS CW, we inoculated three microcosms with two strains of extended-spectrum beta-lactamase producing Escherichia coli (ESBL E. coli) belonging to two genotypes. Microcosms were composed of two sediments collected at two locations of an FWS CW from which the strains were isolated. Phragmites were planted in one of the microcosms. The survival curves of the two strains were close regardless of the genotype and the type of sediment. After a rapid decline, both strains were able to survive at low level in the sediments for 50 days. Their fate was not affected by the presence of phragmites. Changes in the bla content and antibiotic resistance of the inoculated strains were observed after three weeks of incubation, indicating that FWS CW sediments are favorable environments for spread of antibiotic resistance genes and for the acquisition of new antibiotic resistance.

In situ continuous monitoring of nitrogen with ion-selective electrodes in a constructed wetland receiving treated wastewater: an operating protocol to obtain reliable data.

Constructed wetlands receiving treated wastewater (CWtw) are placed between wastewater treatment plants and receiving water bodies, under the perception that they increase water quality. A better understanding of the CWtw functioning is required to evaluate their real performance. To achieve this, in situ continuous monitoring of nitrate and ammonium concentrations with ion-selective electrodes (ISEs) can provide valuable information. However, this measurement needs precautions to be taken to produce good data quality, especially in areas with high effluent quality requirements. In order to study the functioning of a CWtw instrumented with six ISE probes, we have developed an appropriate methodology for probe management and data processing. It is based on an evaluation of performance in the laboratory and an adapted field protocol for calibration, data treatment and validation. The result is an operating protocol concerning an acceptable cleaning frequency of 2 weeks, a complementary calibration using CWtw water, a drift evaluation and the determination of limits of quantification (1 mgN/L for ammonium and 0.5 mgN/L for nitrate). An example of a 9-month validated dataset confirms that it is fundamental to include the technical limitations of the measuring equipment and set appropriate maintenance and calibration methodologies in order to ensure an accurate interpretation of data.

Update on therapeutic approaches for invasive fungal infections in adults.

Invasive fungal infections are increasingly encountered with the expansion of iatrogenic immunosuppression, including not only solid organ and hematopoietic stem cell transplant recipients but also patients with malignancies or autoimmune diseases receiving immunomodulatory therapies, such as Bruton Tyrosine Kinase (BTK) inhibitor. Their attributable mortality remains elevated, part of which is a contribution from globally emerging resistance in both molds and yeasts. Because antifungal susceptibility test results are often unavailable or delayed, empiric and tailored antifungal approaches including choice of agent(s) and use of combination therapy are heterogeneous and often based on clinician experience with knowledge of host's net state of immunosuppression, prior antifungal exposure, antifungal side effects and interaction profile, clinical severity of disease including site(s) of infection and local resistance data. In this review, we aim to summarize previous recommendations and most recent literature on treatment of invasive mold and yeast infections in adults to guide optimal evidence-based therapeutic approaches. We review the recent data that support use of available antifungal agents, including the different triazoles that have now been studied in comparison to previously preferred agents. We discuss management of complex infections with specific emerging fungi such as Scedosporium spp., Fusarium spp., Trichosporon asahii, and Candida auris. We briefly explore newer antifungal agents or formulations that are now being investigated to overcome therapeutic pitfalls, including but not limited to olorofim, rezafungin, fosmanogepix, and encochleated Amphotericin B. We discuss the role of surgical resection or debridement, duration of treatment, follow-up modalities, and need for secondary prophylaxis, all of which remain challenging, especially in patients chronically immunocompromised or awaiting more immunosuppressive therapies.

Complexities and benefits of adopting next-generation sequencing-based tuberculosis diagnostics: a qualitative study among stakeholders in low and high-income countries.

OBJECTIVES: To clarify perceived benefits, barriers and facilitators of Mycobacterium tuberculosis next-generation sequencing implementation in Madagascar and Canada, towards informing implementation of this diagnostic technology in public health agencies and clinical settings in and beyond these settings. DESIGN: This qualitative study involved conducting semistructured interviews with key stakeholders engaged with next-generation sequencing implementation in Madagascar and Canada. Team-based descriptive analysis supported by Nvivo V.12.0 was used to identify key themes. SETTING: The study was conducted with participants involved at the clinical, diagnostic and surveillance levels of tuberculosis (TB) management from Madagascar and Canada. PARTICIPANTS: Eighteen participants were interviewed (nine Madagascar and nine Canada) and included individuals purposively sampled based on involvement with TB surveillance, laboratory diagnosis and clinical management. RESULTS: The following five themes emerged in the analysis of Malagasy and Canadian interviews: (1) heterogeneity in experience with established TB diagnostics, (2) variable understanding of new sequencing-based diagnostics potential; (3) further evidence as being key to expand adoption; (4) ethical arguments and concerns; (5) operational and system-level considerations. CONCLUSION: There persists important lack of familiarity with TB next-generation sequencing (TB NGS) applications among stakeholders in Canada and Madagascar. This translates into skepticism on the evidence underlying its use and its true potential value added within global public health systems. If deployed, TB NGS testing should be integrated with clinical and surveillance programmes. Although this is perceived as a priority, leadership and funding responsibilities for this integration to happen remains unclear to clinical, laboratory and public health stakeholders.

Wastewater data from individual homes: Quantitative and qualitative measurements.

The data article is related to the generation of raw wastewater from 15 single-family dwellings. Such a dataset is rare. They are complicated to set up due to the technical difficulty of deriving a representative sample of this kind of pollution, composed of suspended solids potentially very coarse in size, compounded by the administrative difficulty of performing these measurements on private property. The data were obtained by means of two distinct and complementary monitoring campaigns: i) continuous measurement of the volumes discharged by three of the 15 dwellings during more than one year, and ii) characterization, in terms of both quality and quantity, of more than 300 raw wastewater samples discharged over 24 consecutive hours by all 15 houses during weekly periods of seven consecutive days, which deliberately included weekend days. Their acquisition methodologies are described. The validation's methodologies, also described, include a R script. The data analysis can be used for i) designing and operating onsite and small wastewater treatment systems and ii) characterising the strictly domestic pollution. Therefore, this data article is associated with the manuscript "Quantification and qualification of the urban domestic pollution discharged per households and per resident".The hydraulic values obtained with continuous measurement are available in two units: in l.s-1 as primary data and in l.h-1 as secondary data. They can be reused at any time step. These elements could be incorporated into future research or innovations related to single-family dwellings. In a general point of view, such data could be introduced in databases used for Life Cycle Assessment. These values can also be used in sanitation (collection, design and operation) and be useful to better specify the potential for the recovery of domestic wastewater.

Fate of phosphorus from treated wastewater in soil-based constructed wetlands.

In France, soil-based constructed wetlands for the discharge of treated wastewater have become a popular technique to both reduce flow to surface receiving water bodies and perform complementary treatments. This study focuses on the fate of phosphorus in three different soils, as well as its assimilation by Phragmites australis. The experimental set-up consisted of three lysimeters containing three soils selected to be representative of those typically found near wastewater treatment plants (i.e. a silt loam Fluvisol, a sandy loam Fluvisol and a sandy-clay loam Technosol). Lysimeters are undisturbed soil monoliths (1.5 m3 in volume), whose masses are continuously monitored in order to obtain an accurate water mass balance. The lysimeters here were intermittently fed for 3.5 days and then left to rest for 3.5 days. The experiment lasted 26 months, including 18 months of feeding with phosphorus (PO4-P, TP) fluxes in and out being monitored along with water content, oxygen content and redox potential at various depths. The quantities of phosphorus stored in the soils and assimilated in the Phragmites australis were measured. Phosphorus fractionation in soils was performed to better understand its distribution and potential remobilization. Low phosphate concentrations were measured at the outlets of all three lysimeters, thereby highlighting satisfactory phosphorus retention in the three soils (removal efficiencies >90%). A significant amount of phosphorus can be exported by harvesting Phragmites australis aerial parts (26%, 17% and 13% of the yearly incoming phosphorus mass for the silt loam Fluvisol, sandy loam Fluvisol and sandy-clay loam Technosol, respectively). The fractionation step served to determine that the phosphorus retained in the soil was primarily bound to iron oxides/hydroxides, calcium and clay. Moreover, it was found to be preferable to hold oxidizing (aerobic) conditions and pH close to neutral in order to maintain conditions under which the complexes formed with phosphorus remain stable.

Applying life cycle assessment to assess the environmental performance of decentralised versus centralised wastewater systems.

Decentralised wastewater management (DWM) systems are deployed in areas where the topography does not allow for gravity flow to a centralised system, or requires a complex and expensive pumping station network. Also, DWM systems are often the only option in rural areas where there are no sewage transport networks. This paper aims at addressing the question of the degree to which DWM systems can be considered as viable alternatives from an environmental point of view using the Life Cycle Assessment (LCA) methodology. First, the environmental sustainability is investigated to identify environmental hotspots in two (nature-based and engineered) onsite DWM systems. Second, DWM scenarios are compared against centralised wastewater management (CWM) scenarios using a whole-systems approach. Finally the boundary conditions under which a given DWM scenario performs better than a CWM scenario are discussed. Results show CWM scenarios were less sustainable than DWM scenarios on the resources endpoint due to their sewer infrastructures, however CWM scenarios performed better than DWM scenarios on the ecosystems quality endpoint due to their well-managed air emissions and discharges. While on human health no clear conclusion could be drawn. Finally, for relatively few households (subject of the study in rural areas) CWM scenarios did not score superior performances compared to DWM scenarios on all three endpoint indicators. Yet for a greater number of households it was impossible to decide in favour of decentralisation because of a lack of favourable consensus on all three endpoint indicators.

Clinical Evaluation of In-House-Produced 3D-Printed Nasopharyngeal Swabs for COVID-19 Testing.

3D-printed alternatives to standard flocked swabs were rapidly developed to provide a response to the unprecedented and sudden need for an exponentially growing amount of diagnostic tools to fight the COVID-19 pandemic. In light of the anticipated shortage, a hospital-based 3D-printing platform was implemented in our institution for the production of swabs for nasopharyngeal and oropharyngeal sampling based on the freely available, open-source design provided to the community by University of South Florida's Health Radiology and Northwell Health System teams as a replacement for locally used commercial swabs. Validation of our 3D-printed swabs was performed with a head-to-head diagnostic accuracy study of the 3D-printed "Northwell model" with the cobas PCR Media® swab sample kit. We observed an excellent concordance (total agreement 96.8%, Kappa 0.936) in results obtained with the 3D-printed and flocked swabs, indicating that the in-house 3D-printed swab could be used reliably in the context of a shortage of flocked swabs. To our knowledge, this is the first study to report on autonomous hospital-based production and clinical validation of 3D-printed swabs.

Pandoraea sp infection in a lung transplant patient and the critical role of MALDI-TOF in accurate bacterial identification.

Diagnosis and clinical management of pulmonary infections in lung transplant patients are challenging. The increased diversity of bacterial species identified from clinical samples with novel proteomics-based systems can further complicate clinical decision making in this highly vulnerable population. Whether newly recognized organisms are colonizers or true pathogens often remains controversial since symptoms causality and impact on lung function is often unknown. We present the case of a 48-year-old female lung transplant patient with Pandoraea sp infection. We review and discuss the role of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for accurate bacterial identification. We report on therapeutic management and clinical outcome.

Il est difficile de diagnostiquer et d'assurer la prise en charge clinique des infections pulmonaires chez les patients ayant une transplantation pulmonaire. La diversité accrue des espèces bactériennes identifiées dans des échantillons cliniques contenant de nouveaux systèmes protéomiques peut compliquer encore les décisions cliniques dans cette population hautement vulnérable. On ne sait pas exactement si les nouvelles formes d'organismes sont des colonisateurs ou de véritables agents pathogènes puisque, dans bien des cas, on ne connaît ni la cause ni l'impact des symptômes sur la fonction pulmonaire. Les auteurs présentent le cas d'une femme de 48 ans ayant une transplantation pulmonaire atteinte d'une infection par une espèce à Pandoraea. Ils analysent et exposent le rôle de la spectrométrie de masse par désorption-ionisation laser assistée par matrice pour bien identifier la bactérie. Ils rendent compte de la prise en charge thérapeutique et des résultats cliniques de cette patiente.

Comparison of SARS-CoV-2 detection from combined nasopharyngeal/oropharyngeal swab samples by a laboratory-developed real-time RT-PCR test and the Roche SARS-CoV-2 assay on a cobas 8800 instrument.

OBJECTIVE: Although several assays have been developed to detect SARS-CoV-2 RNA in clinical specimens, their relative performance is unknown. METHODS: The concordance between the cobas 8800 SARS-CoV-2 and a laboratory developed (LD) reverse transcriptase-polymerase chain reaction (RT-PCR) assay was assessed on 377 combined nasopharyngeal/oropharyngeal swabs in Hanks medium. RESULTS: The positive and negative agreement between these assays were 99.3 % (95 % CI, 97.3-99.9) and 77.1 % (95 % CI, 67.7-84.4), respectively, for an overall agreement of 93.6 % (95 % CI, 90.7-95.7) beyond random chance (kappa of 0.82, 95 % CI, 0.75-0.85). Of the 22 samples positive by cobas SARS-CoV-2 only, 9 were positive only for ORF-1 gene and had Cycle thresholds (Ct) > 35.1, 8 were positive only for the E gene with Ct > 35.5 and 5 were positive for both targets with Ct > 33.9. Samples positive only with the cobas assay were more often positive with only one gene target (77.3 %) than samples positive in both assays (16.9 %, p < 0.0001). Ct values in the cobas SARS-CoV-2 assay were significantly higher in the 279 samples testing positive in both assays (32.9 %, 95 % CI 32.3-33.6) compared to the 22 samples with discordant results (36.6 %, 95 % CI 36.2-37.1; p = 0.0009). An excellent correlation (r2 = 0.98) was obtained between Ct values of the ORF-1 and E targets in the cobas assays and a good correlation was obtained between LD RT-PCR test and cobas SARS CoV-2 ORF-1 target (r2 = 0.82). CONCLUSION: Our study demonstrated an excellent concordance between a LD RT-PCR and the cobas SARS-CoV-2 tests on the 8800 platform.