The science behind the nose: correlating volatile organic compound characterisation with canine biodetection of COVID-19.

Background: The SARS-CoV-2 pandemic stimulated the advancement and research in the field of canine scent detection of COVID-19 and volatile organic compound (VOC) breath sampling. It remains unclear which VOCs are associated with positive canine alerts. This study aimed to confirm that the training aids used for COVID-19 canine scent detection were indeed releasing discriminant COVID-19 VOCs detectable and identifiable by gas chromatography (GC-MS). Methods: Inexperienced dogs (two Labradors and one English Springer Spaniel) were trained over 19 weeks to discriminate between COVID-19 infected and uninfected individuals and then independently validated. Getxent tubes, impregnated with the odours from clinical gargle samples, used during the canines' maintenance training process were also analysed using GC-MS. Results: Three dogs were successfully trained to detect COVID-19. A principal components analysis model was created and confirmed the ability to discriminate between VOCs from positive and negative COVID-19 Getxent tubes with a sensitivity of 78% and a specificity of 77%. Two VOCs were found to be very predictive of positive COVID-19 cases. When comparing the dogs with GC-MS, F1 and Matthew's correlation coefficient, correlation scores of 0.69 and 0.37 were observed, respectively, demonstrating good concordance between the two methods. Interpretation: This study provides analytical confirmation that canine training aids can be safely and reliably produced with good discrimination between positive samples and negative controls. It is also a further step towards better understanding of canine odour discrimination of COVID-19 as the scent of interest and defining what VOC elements the canines interpret as "essential".

Severe hypercalcemia as a result of disseminated Candida krusei infection.

Candida krusei disseminated infection is a rare complication of protracted neutropenia. Herein, we report a case of a 31-year-old male with relapsed acute myeloid leukemia who developed Candida krusei fungemia with cutaneous, ocular, splenic, renal, bone marrow and osseous involvement leading to severe hypercalcemia, treated with parenteral antifungals followed by oral ibrexafungerp.

Quick versus Quantitative: Evaluation of Two Commercial Real-Time PCR Assays for the Detection of Pneumocystis jirovecii from Bronchoalveolar Lavage Fluids.

Two commercial real-time PCR assays for the detection of Pneumocystis jirovecii were compared, the quantitative RealStar P. jirovecii assay and the qualitative DiaSorin P. jirovecii assay, the latter of which can be used without nucleic acid extraction. Archived bronchoalveolar lavage (BAL) specimens (n = 66), previously tested by molecular methods, were tested by both assays, and the results were compared to the respective original result. The RealStar P. jirovecii assay demonstrated good positive percent agreement (PPA) (90% [95% confidence interval (CI), 72 to 97%]; 27/30) and negative percent agreement (NPA) (100% [95% CI, 88 to 100%]; 36/36) with the reference method. The DiaSorin P. jirovecii assay concordantly detected P. jirovecii in 19 of 24 positive BAL samples (PPA = 73% [95% CI, 52 to 88%]). All negative BAL samples gave concordant results (NPA = 100% [95% CI, 87 to 100%]; 34/34). Discordant results occurred mostly in samples with low fungal loads. In conclusion, the RealStar assay demonstrated good concordance with reference results, and the DiaSorin P. jirovecii assay performed well for negative BAL and positive BAL samples with P. jirovecii concentrations of greater than 260 copies/mL. IMPORTANCE Pneumonia, caused by the opportunistic fungus Pneumocystis jirovecii, poses a significant risk for immunocompromised individuals. Laboratory testing for P. jirovecii is progressively shifting toward the use of molecular tests such as real-time PCR; however, this is often performed at reference laboratories. Many frontline laboratories are looking into improving their service and reducing turnaround times for obtaining P. jirovecii results by bringing molecular P. jirovecii testing in-house. We evaluated and compared two commercial real-time PCR assays with different workflows for the detection of P. jirovecii from bronchoalveolar lavage specimens. The RealStar P. jirovecii assay requires nucleic acid extraction and provides a quantification of fungal load for positive samples. The DiaSorin P. jirovecii assay offers a simple workflow without nucleic extraction from patient samples and qualitative results. Results from this study provide valuable information on performance and workflow considerations for laboratories that wish to implement P. jirovecii molecular testing.

Abbott ID NOW™ COVID-19 assay: do not discard the swab.

We compared the performance of ID NOW™ COVID-19 assay nasal swabs with RT-PCR of nasopharyngeal swabs for SARS-CoV-2 in an outbreak setting, determining whether addition of RT-PCR of residual nasal swabs (rNS) (post ID NOW™ elution) would increase overall analytic sensitivity. Devices were placed at 2 long term and 1 acute care sites and 51 participants were recruited. Prospective paired nasopharyngeal and nasal samples were collected for RT-PCR and ID NOW™.  ID NOW™ had a positive and negative categorical agreement of 86% and 93% compared to RT-PCR of nasopharyngeal swabs. Sensitivity and specificity of the ID NOW™ was 86% and 100%, positive and negative predictive value was 100% and 95% (COVID-19 positivity rate: 8%). Addition of rNS RT-PCR increased the positive and negative categorical agreement to 93% and 97%. Based on these results, we propose an alternative workflow which includes complementary testing of rNS on a secondary assay.

Automated 16S Sequencing Using an R-Based Analysis Module for Bacterial Identification.

Sanger sequencing of the 16S rRNA gene is routinely used for the identification of bacterial isolates. However, this method is still performed mostly in more-specialized reference laboratories, and traditional protocols can be labor intensive. In this study, 99 clinical bacterial isolates were used to validate a fast, simplified, and largely automated protocol for 16S sequencing. The workflow combines real-time PCR of the first 500 bp of the bacterial 16S rRNA gene and amplicon sequencing on an automated, cartridge-based sequence analyzer. Sequence analysis, NCBI BLAST search, and result interpretation were performed using an automated R-based script. The automated workflow and R analysis described here produced results equal to those of manual sequence analysis. Of the 96 sequences with adequate quality, 90 were concordantly identified to the genus (n = 62) or species level (n = 28) compared with routine laboratory identification of the organism. One organism identification was discordant, and 5 resulted in an inconclusive identification. For sequences that gave a valid result, the overall accuracy of identification to at least the genus level was 98.9%. This simplified sequencing protocol provides a standardized approach to clinical 16S sequencing, analysis, and quality control that would be suited to frontline clinical microbiology laboratories with minimal experience. IMPORTANCE Sanger sequencing of the 16S rRNA gene is widely used as a diagnostic tool for bacterial identification, especially in cases where routine diagnostic methods fail to provide an identification, for organisms that are difficult to culture, or from specimens where cultures remain negative. Our simplified protocol is tailored toward use in frontline laboratories with little to no experience with sequencing. It provides a highly automated workflow that can deliver fast results with little hands-on time. Implementing 16S sequencing in-house saves additional time that is otherwise required to send out isolates/specimens for identification to reference laboratories. This makes results available much faster to physicians who can in turn initiate or adjust patient treatment accordingly.

In search of COVID-19: The ability of biodetection canines to detect COVID-19 odours from clinical samples.

BACKGROUND: COVID-19 continues to be a public health concern and the demand for fast and reliable screening tests remains. SARS-CoV-2 infection in humans generates a specific volatile organic compound signature; this 'volatilome' could be used to deploy highly trained canine scent detection teams if they could reliably detect odours from infected individuals. METHODS: Two dogs were trained over 19 weeks to discriminate between the odours produced by breath, sweat, and gargle specimens collected from SARS-CoV-2 infected and uninfected individuals. Third party validation was conducted in a randomized double-blinded controlled manner using fresh odours obtained from different patients within 10 days of their first positive SARS-CoV-2 molecular result. RESULTS: Cumulatively, the dogs completed 299 training sessions on odours from 108 unique participants. Validation was conducted over 2 days with 120 new odours. Twenty-four were odours collected from SARS-CoV-2 positive individuals (8 gargle, 8 sweat, and 8 breath); 21 were from SARS-CoV-2 negative individuals (5 gargle, 8 sweat, and 8 breath) and the remaining 75 were odours that the dogs could have associated with the target odour during training. The dogs were able to identify odours from positive specimens with an overall sensitivity of 100% and a specificity of 87.5%. Considering a community prevalence of 10%, the combined negative predictive value of the dogs was 100% and the positive predictive value was 47.1%. CONCLUSIONS: Multiple dogs can be trained to accurately detect SARS-CoV-2 positive individuals. Future research is required to determine how and when canine scent detection teams should be deployed.

HISTORIQUE: La COVID-19 continue d'être une préoccupation sanitaire, et la demande de tests de dépistage rapides et fiables se maintient. L'infection par le SRAS-CoV-2 chez les humains produit une signature composée organique volatile bien précise. Ce « volatilome ¼ pourrait être utilisé pour déployer des équipes canines hautement formées et spécialisées dans la détection des odeurs afin d'établir si elles peuvent détecter les odeurs des personnes infectées avec fiabilité. MÉTHODOLOGIE: Deux chiens ont été formés pendant 19 semaines pour distinguer les odeurs émanantes des échantillons d'haleine, de sueur et de gargarisme prélevés chez des personnes infectées et non infectées par le SRAS-CoV-2. Les chercheurs ont effectué une validation par des tiers dans le cadre d'une étude contrôlée randomisée à double insu au moyen d'odeurs fraîches obtenues auprès de divers patients dans les dix jours suivant le premier résultat moléculaire positif au SRAS-CoV-2. RÉSULTATS: Dans l'ensemble, les chiens ont effectué 299 séances de formation sur les odeurs de 108 participants uniques. La validation a eu lieu sur deux jours à partir de 120 nouvelles odeurs. Ainsi, 24 odeurs provenaient de personnes positives au SRAS-CoV-2 (8 échantillons de gargarisme, 8 de sueur et 8 d'haleine); 21 provenaient de personnes négatives au SRAS-CoV-2 (5 échantillons de gargarisme, 8 de sueur et 8 d'haleine) et les 75 autres étaient des odeurs que les chiens avaient pu associer à l'odeur cible pendant la formation. Les chiens ont été en mesure de dépister les odeurs des échantillons positifs selon une sensibilité globale de 100 % et une spécificité de 87,5 %. Étant donné une prévalence communautaire de 10 %, la valeur prédictive négative combinée des chiens s'élevait à 100 % et la valeur prédictive positive, à 47,1 %. CONCLUSIONS: De nombreux chiens peuvent être formés pour dépister avec exactitude les personnes positives au SRAS-CoV-2. De futures recherches devront être réalisées pour déterminer quand et comment déployer ces équipes canines spécialisées en biodétection.

Evaluation of the BioFire® COVID-19 test and Respiratory Panel 2.1 for rapid identification of SARS-CoV-2 in nasopharyngeal swab samples.

The BioFire® COVID-19 Test and Respiratory Panel 2.1 (RP2.1) are rapid, fully automated assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs. In the case of the RP2.1, an additional 21 viral and bacterial pathogens can be detected. Both tests have received emergency use authorization from the U.S. Food & Drug Administration and Interim Order authorization from Health Canada for use in clinical laboratories. We evaluated the performance characteristics of these tests in comparison to a laboratory-developed real-time PCR assay targeting the viral RNA-dependent RNA polymerase and E genes. A total of 78 tests were performed using the BioFire COVID-19 Test, including 30 clinical specimens and 48 tests in a limit of detection study; 57 tests were performed using the RP2.1 for evaluation of SARS-CoV-2 detection, including 30 clinical specimens and 27 tests for limit of detection. Results showed 100% concordance between the BioFire assays and the laboratory-developed test for all clinical samples tested, and acceptable performance of both BioFire assays at their stated limits of detection. Conclusively, the BioFire COVID-19 Test and RP2.1 are highly sensitive assays that can be effectively used in the clinical laboratory for rapid SARS-CoV-2 testing.

An unusual case of abdominal pain and splenomegaly in a paediatric patient.

Fusobacterium species are members of the oral microbiota and have been found to cause a wide spectrum of opportunistic infections. We describe the case of a previously healthy teenager with a large splenic abscess secondary to Fusobacterium nucleatum, successfully managed with percutaneous drainage and intravenous antibiotics. Identification of the organism was achieved using anaerobic culture of the aspirated fluid and matrix-assisted laser desorption/ionization time of flight, later confirmed by 16S ribosomal RNA metagenomic sequencing of the fluid. Fusobacteria are typically associated with oropharyngeal infections but are very rarely implicated in splenic abscesses. Aerobic and anaerobic blood cultures should be drawn when an intra-abdominal infection is suspected in a paediatric patient, and empiric antimicrobial therapy should be administered with coverage for gram-positive, gram-negative, and anaerobic bacteria.

Needle in a haystack: Looking for tuberculosis in a low-incidence setting.

Background: Canada is a low-incidence country for tuberculosis (TB). The BC Public Health Laboratory diagnostic algorithm for pulmonary TB includes acid fast bacilli (AFB) smear and mycobacterial culture of all submitted sputa. TB nucleic acid amplification testing (NAT) is routinely performed on AFB-smear-positive (AFB+) sputa only. We assessed the laboratory-associated costs of implementing the international recommendations for TB NAT on AFB-smear-negative (AFB-) sputa. Methods: Two data sets were obtained: (1) all AFB- samples for a 3-year period (October 1, 2014-September 30, 2017) and (2) all AFB-, TB-culture-positive samples for the same period. One AFB- sample/patient from each defined diagnostic set of sputa was deemed eligible for TB NAT. To stratify patients by ordering location, a 1-year subset of data (October 1, 2016-September 30, 2017) was examined. Results: In the 3-year period, 0.7% of all diagnostic sets were AFB- and culture-positive. In the 1-year period, the provincial TB Services clinics submitted 26% of all AFB- samples received, but these constituted 78% of AFB-, culture-positive samples. Conclusions: The annual cost of TB NAT on one AFB- sputum sample from each eligible diagnostic set would total approximately $247,000. Targeting only TB Services clinic patients would reduce this cost to approximately $64,000/year while capturing more than 75% of AFB-, culture-positive patients. On the basis of our provincial positivity rate, it would cost approximately $6,000 to provide an early TB diagnosis for an AFB-, culture-positive patient. The cost-effectiveness to public health of this approach in a TB low-incidence setting needs to be carefully evaluated.

Historique: Le Canada est un pays à faible incidence de tuberculose. L'algorithme diagnostique de tuberculose pulmonaire du BC Public Health Laboratory inclut la recherche des bacilles acido-alcoolo-résistants (BAAR) par frottis et la culture mycobactérienne de toutes les expectorations soumises. Le test d'amplification de l'acide nucléique (TAN) pour dépister la tuberculose (TAN TB) est effectué systématiquement, mais seulement sur les expectorations positives au BAAR par frottis (BAAR+). Les chercheurs ont évalué quelle somme le laboratoire devrait investir pour mettre en œuvre les recommandations internationales visant l'utilisation du TAN TB sur des expectorations négatives BAAR par frottis (BAAR-). Méthodologie: Les chercheurs ont obtenu deux groupes de données : 1) tous les échantillons BAAR­ sur une période de trois ans (du 1er octobre 2014 au 30 septembre 2017) et 2) tous les échantillons BAAR­ dont la culture était positive à la tuberculose pendant la même période. Un échantillon de BAAR­ par patient de chaque groupe diagnostique d'expectoration était considéré comme admissible au TAN TB. Pour stratifier les patients selon la provenance du test, les chercheurs ont examiné un sous-groupe de données sur un an (du 1er octobre 2016 au 30 septembre 2017). Résultats: Pendant la période de trois ans, 0,7 % de tous les groupes diagnostiques étaient BAAR­ et positifs à la culture. Pendant la période d'un an, les cliniques provinciales de services pour la tuberculose ont soumis 26 % de tous les échantillons BAAR­ reçus, mais ils représentaient 78 % des échantillons BAAR­ positifs aux cultures. Conclusions: Le coût annuel du TAN TB sur un échantillon d'expectoration BAAR­ de chaque groupe diagnostique admissible totaliserait environ 247 000 $. Si on ciblait seulement les patients ayant consulté des services pour la tuberculose, ce coût fléchirait à environ 64 000 $ par année, mais saisirait plus de 75 % des patients BAAR­ dont la culture est positive. D'après le taux de positivité provinciale, un diagnostic précoce de tuberculose chez un patient BAAR­ positif à la culture coûterait environ 6 000 $. Le rapport coût-efficacité de cette approche pour la santé publique dans les milieux à faible incidence de tuberculose devra faire l'objet d'une évaluation attentive.

First reported outbreak of the emerging pathogen Candida auris in Canada.

BACKGROUND: Candida auris was first described in Japan in 2009 and has since been detected in over 40 countries. The yeast is concerning for multiple reasons, primarily: (1) challenges with accurate identification; (2) reported multidrug resistance; (3) published mortality rates of 30%-60%; and (4) persistence in the environment associated with human transmission. We report the emergence of a healthcare-associated cluster in the Greater Vancouver area in 2018 and describe the measures implemented to contain its transmission. METHODS: Cases were identified through passive and ring surveillance of affected wards. Positive isolates were sent to provincial and national reference laboratories for confirmation and genomic characterization. Extensive infection control measures were implemented immediately after the initial case was identified. RESULTS: Four cases were identified during the outbreak. In a 4-month period, over 700 swabs were collected in order to screen 180 contacts. Whole genome sequencing concluded that all isolates clustered together and belonged to the South Asian clade. No isolates harbored FKS gene mutations associated with resistance to echinocandins. Infection control measures, including surveillance, education, cleaning and/or disinfection, patient cohorting, isolation, and hand hygiene, effectively contained the outbreak; it was declared over within 2 months. CONCLUSIONS: The spread of C auris in healthcare facilities has not spared Canadian institutions. Our experience demonstrates that strict infection control measures combined with microbiological screening can effectively halt transmission in healthcare centers. The necessity of active prospective screening remains unclear.

New Tools to Test Stool: Managing Travelers' Diarrhea in the Era of Molecular Diagnostics.

Travelers' diarrhea affects up to 60% of visitors to tropical and subtropical regions. Although symptoms are generally self-limited, some infections are associated with significant morbidity and occasional mortality. Newer molecular diagnostic techniques allow for highly sensitive, specific, and expeditious testing of a wide range of potential pathogens. Identification of the causative pathogen of travelers' diarrhea allows for targeted therapy and management and a reduction in empiric broad-spectrum coverage.

Quantitative computed tomography measures of pectoralis muscle area and disease severity in chronic obstructive pulmonary disease. A cross-sectional study.

RATIONALE: Muscle wasting in chronic obstructive pulmonary disease (COPD) is associated with a poor prognosis and is not readily assessed by measures of body mass index (BMI). BMI does not discriminate between relative proportions of adipose tissue and lean muscle and may be insensitive to early pathologic changes in body composition. Computed tomography (CT)-based assessments of the pectoralis muscles may provide insight into the clinical significance of skeletal muscles in smokers. OBJECTIVES: We hypothesized that objective assessment of the pectoralis muscle area on chest CT scans provides information that is clinically relevant and independent of BMI. METHODS: Data from the ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) Study (n = 73) were used to assess the relationship between pectoralis muscle area and fat-free mass. We then used data in a subset (n = 966) of a larger cohort, the COPDGene (COPD Genetic Epidemiology) Study, to explore the relationship between pectoralis muscle area and COPD-related traits. MEASUREMENTS AND MAIN RESULTS: We first investigated the correlation between pectoralis muscle area and fat-free mass, using data from a subset of participants in the ECLIPSE Study. We then further investigated pectoralis muscle area in COPDGene Study participants and found that higher pectoralis muscle area values were associated with greater height, male sex, and younger age. On subsequent clinical correlation, compared with BMI, pectoralis muscle area was more significantly associated with COPD-related traits, including spirometric measures, dyspnea, and 6-minute-walk distance (6MWD). For example, on average, each 10-cm(2) increase in pectoralis muscle area was associated with a 0.8-unit decrease in the BODE (Body mass index, Obstruction, Dyspnea, Exercise) index (95% confidence interval, -1.0 to -0.6; P < 0.001). Furthermore, statistically significant associations between pectoralis muscle area and COPD-related traits remained even after adjustment for BMI. CONCLUSIONS: CT-derived pectoralis muscle area provides relevant indices of COPD morbidity that may be more predictive of important COPD-related traits than BMI. However, the relationship with clinically relevant outcomes such as hospitalization and death requires additional investigation. Pectoralis muscle area is a convenient measure that can be collected in the clinical setting in addition to BMI.