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.

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.

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.

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.

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.