Alveolar Echinococcus in a 70-year-old man in Ontario.

Background: Alveolar echinococcus, caused by the tapeworm Echinococcus multilocularis, mimics hepatic malignancy, and carries a mortality rate exceeding 90% in untreated patients. Methods: Diagnosis of E. multilocularis infection is established through clinical, radiographic, and microbiological assessments. Currently available laboratory diagnostics in Ontario are fresh tissue microscopy and histopathology. However, genus-specific Echinococcus enzyme-linked immunosorbent assay (ELISA) serology as well as confirmatory testing with species-specific serology and E. multilocularis polymerase chain reaction (PCR) can be obtained from external reference laboratories. Results: The article presents the first case report of human alveolar echinococcus in Ontario. We outline the multidisciplinary approach of diagnosis as well as surgical and medical management of E. multilocularis infection in a 70-year-old man in Ontario. We describe prior literature of alveolar echinococcus in Canadian settings and highlight its emerging nature with recent human case clusters in the Prairies and reports of E. multilocularis in recent veterinary literature in Ontario. Conclusion: E. multilocularis is an emerging parasitic infection in Canadian settings including Ontario. Clinicians should be aware of the emergence of this invasive infection, especially in those with close contact to canids.

Historique: Causée par le ténia Echinococcus multilocularis, l'échinococcose alvéolaire, qui imite le cancer du foie, est associée à un taux de décès de plus de 90 % chez les patients non traités. Méthodologie: Le diagnostic d'infection par l'E multilocularis est posé par une évaluation clinique, radiographique et microbiologique. La microscopie sur tissus frais et l'histopathologie sont les diagnostics microbiologiques actuellement offerts en Ontario. Cependant, il est possible d'obtenir une analyse sérologique par la méthode d'immunoabsorption enzymatique (ELISA) spécifique du genre Echinococcus ainsi que des tests de confirmation par analyse sérologique spécifique à l'espèce et par amplification en chaîne par polymérase (PCR) de l'E multilocularis auprès de laboratoires de référence externes. Résultats: L'article présente le premier rapport de cas d'échinococcose alvéolaire humaine en Ontario. Les chercheurs soulignent l'approche multidisciplinaire du diagnostic, de même que la prise en charge chirurgicale et médicale de l'infection à E multilocularis chez un homme de 70 ans de l'Ontario. Ils décrivent les publications scientifiques antérieures sur l'échinococcose alvéolaire au Canada et soulignent l'émergence de cette maladie parasitaire dans une récente grappe de cas humains des Prairies, de même que les comptes rendus de cas d'E multilocularis dans les récentes publications vétérinaires de l'Ontario. Conclusion: L'E multilocularis est une infection parasitaire en émergence au Canada, y compris en Ontario. Les cliniciens devraient être informés de l'émergence de cette infection invasive, notamment chez les personnes en contact étroit avec des canidés.

Salmonella Vitkin Outbreak Associated with Bearded Dragons, Canada and United States, 2020-2022.

We identified 2 cases of Salmonella enterica serovar Vitkin infection linked by whole-genome sequencing in infants in Ontario, Canada, during 2022. Both households of the infants reported having bearded dragons as pets. The outbreak strain was also isolated from an environmental sample collected from a patient's bearded dragon enclosure. Twelve cases were detected in the United States, and onset dates occurred during March 2021-September 2022 (isolates related to isolates from Canada within 0-9 allele differences by core-genome multilocus sequence typing). Most US patients (66.7%) were <1 year of age, and most (72.7%) had reported bearded dragon exposure. Hospitalization was reported for 5 (38.5%) of 13 patients. Traceback of bearded dragons identified at least 1 potential common supplier in Southeast Asia. Sharing rare serovar information and whole-genome sequencing data between Canada and the United States can assist in timely identification of outbreaks, including those that might not be detected through routine surveillance.

Viral dynamics of the SARS-CoV-2 Omicron Variant in Paediatric Patients; A prospective cohort study.

BACKGROUND: There are limited data on the viral dynamics of SARS-CoV-2 in children. Understanding viral load changes over the course of illness and duration of viral shedding may provide insight into transmission dynamics to inform public health and infection control decisions. METHODS: We conducted a prospective cohort study of children 18 years and younger with PCR confirmed SARS-CoV-2 between February 1, 2022 and March 14, 2022. SARS-CoV-2 testing occurred on daily samples for 10 days; a subset of participants completed daily rapid antigen testing (RAT). Viral RNA trajectories were described in relation to symptom onset and resolution. The associations between both time since symptom onset/resolution and non-infectious viral load were evaluated using a Cox proportional hazards model. FINDINGS: Among 101 children aged 2 to 17 years, the median time to study-defined non-infectious viral load was 5 days post symptom onset, with 75% meeting this threshold by 7 days, and 90% by 10 days. On the day of and day after symptom resolution, 43 of 87 (49%) and 52 (60%) had met the non-infectious thresholds, respectively. Of the 50 participants completing RAT, positivity at symptom onset and on the day after symptom onset was 67% (16/24) and 75% (14/20). On the first day where the non-infectious threshold was met, 61% (n = 27/44) of participant RAT results were positive. INTERPRETATION: Children often met the study-defined non-infectiousness threshold on the day after symptom resolution. RAT tests were often negative early in the course of illness and should not be relied on to exclude infection. CLINICAL TRIALS REGISTRATION: NCT05240183.

Case Report: A Case of Bone Marrow Necrosis and Hyperinflammation in a 10-Year-Old Boy after Plasmodium falciparum Infection.

A 10-year-old boy with sickle cell disease (SCD) type SC presented with fever and abdominal pain after travel to Ghana and was diagnosed with Plasmodium falciparum infection. Despite adequate antimalarial treatment, he developed evidence of hyperinflammation with marked elevated ferritin, C-reactive protein, and triglycerides and subsequent bone marrow necrosis, characterized by elevated nucleated red blood cells and significant bone pain. This case report highlights the possible association between malaria and bone marrow necrosis in patients with SCD. Important considerations in treatment and workup of patients presenting with malaria and hyperinflammation are discussed.

Geographic clustering of travel-acquired infections in Ontario, Canada, 2008-2020.

As the frequency of international travel increases, more individuals are at risk of travel-acquired infections (TAIs). In this ecological study of over 170,000 unique tests from Public Health Ontario's laboratory, we reviewed all laboratory-reported cases of malaria, dengue, chikungunya, and enteric fever in Ontario, Canada between 2008-2020 to identify high-resolution geographical clusters for potential targeted pre-travel prevention. Smoothed standardized incidence ratios (SIRs) and 95% posterior credible intervals (CIs) were estimated using a spatial Bayesian hierarchical model. High- and low-incidence areas were described using data from the 2016 Census based on the home forward sortation area of patients testing positive. A second model was used to estimate the association between drivetime to the nearest travel clinic and incidence of TAI within high-incidence areas. There were 6,114 microbiologically confirmed TAIs across Ontario over the study period. There was spatial clustering of TAIs (Moran's I = 0.59, p<0.0001). Compared to low-incidence areas, high-incidence areas had higher proportions of immigrants (p<0.0001), were lower income (p = 0.0027), had higher levels of university education (p<0.0001), and less knowledge of English/French languages (p<0.0001). In the high-incidence Greater Toronto Area (GTA), each minute increase in drive time to the closest travel clinic was associated with a 3% reduction in TAI incidence (95% CI 1-6%). While urban neighbourhoods in the GTA had the highest burden of TAIs, geographic proximity to a travel clinic in the GTA was not associated with an area-level incidence reduction in TAI. This suggests other barriers to seeking and adhering to pre-travel advice.

A Ten-Year Retrospective Survey of Antimicrobial Susceptibility Patterns among Salmonella enterica subsp. enterica Serovar Typhi Isolates in Ontario, Canada.

The epidemiology and treatment of typhoid fever are complicated by the emergence and spread of Salmonella enterica subsp. enterica serovar Typhi lineages with resistance to many antimicrobial agents critical for therapy. Current information on the susceptibility patterns of S. Typhi isolates identified in regions where typhoid fever is not endemic is important as these are often acquired after traveling to countries of endemicity where resistant strains circulate. Here, we report a 10-year retrospective survey of S. Typhi antimicrobial susceptibility patterns among 858 unique patient isolates that underwent reference laboratory testing in Ontario, Canada, between 2010 and 2019. Antimicrobial susceptibility patterns remained stable for ampicillin (average, 78.7% susceptible), azithromycin (average, 99.4% susceptible) ertapenem (average, 100.0% susceptible), meropenem (average, 100.0% susceptible), and trimethoprim-sulfamethoxazole (average, 78.2% susceptible) during the study period; however, nonsusceptibility to ciprofloxacin and ceftriaxone increased. While ceftriaxone-resistant isolates comprised 1.6% of the total isolates overall, they represented 10.1% of the total isolates tested in 2019, indicating a significant increase over time. Our findings suggest that when selecting empirical therapy, health care providers should strongly consider current trends in antimicrobial susceptibility and investigate the patient's exposure risk to gauge whether a suspected typhoid infection may be caused by a potentially resistant S. Typhi strain. IMPORTANCE This work provides an updated summary of the antimicrobial susceptibility patterns among Salmonella Typhi strains isolated from patients in Ontario, Canada.

Monkeypox Virus Detection in Different Clinical Specimen Types.

A global monkeypox outbreak began in May 2022. Limited data exist on specimen type performance in associated molecular diagnostics. Consequently, a diverse range of specimen sources were collected in the initial weeks of the outbreak in Ontario, Canada. Our clinical evaluation identified skin lesions as the optimal diagnostic specimen source.

Genotyping Canadian Cyclospora cayetanensis Isolates to Supplement Cyclosporiasis Outbreak Investigations.

Cyclospora cayetanensis is an emerging foodborne parasite that causes cyclosporiasis, an enteric disease of humans. Domestically acquired outbreaks have been reported in Canada every spring or summer since 2013. To date, investigations into the potential sources of infection have relied solely on epidemiological data. To supplement the epidemiological data with genetic information, we genotyped 169 Canadian cyclosporiasis cases from stool specimens collected from 2010 to 2021 using an existing eight-marker targeted amplicon deep (TADS) scheme specific to C. cayetanensis as previously described by the US Centers for Disease Control and Prevention (CDC). This is the first study to genotype Canadian Cyclospora cayetanensis isolates, and it focuses on evaluating the genotyping performance and genetic clustering. Genotyping information was successfully collected with at least part of one of the markers in the TADS assay for 97.9% of specimens, and 81.1% of cyclosporiasis cases met the minimum requirements to genetically cluster into 20 groups. The performance of the scheme suggests that examining cyclosporiasis cases genetically will be a valuable tool for supplementing epidemiological outbreak investigations and to minimize further infections. Further research is required to expand the number of discriminatory markers to improve genetic clustering.

Real-Time RT-PCR Allelic Discrimination Assay for Detection of N501Y Mutation in the Spike Protein of SARS-CoV-2 Associated with B.1.1.7 Variant of Concern.

The N501Y amino acid mutation caused by a single point substitution A23063T in the spike gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is possessed by three variants of concern (VOCs), B.1.1.7, B.1.351, and P.1. A rapid screening tool using this mutation is important for surveillance during the coronavirus disease 2019 (COVID-19) pandemic. We developed and validated a single nucleotide polymorphism real-time reverse transcription PCR assay using allelic discrimination of the spike gene N501Y mutation to screen for potential variants of concern and differentiate them from SARS-CoV-2 lineages without the N501Y mutation. A total of 160 clinical specimens positive for SARS-CoV-2 were characterized as mutant (N501Y) or N501 wild type by Sanger sequencing and were subsequently tested with the N501Y single nucleotide polymorphism real-time reverse transcriptase PCR assay. Our assay, compared to Sanger sequencing for single nucleotide polymorphism detection, demonstrated positive percent agreement of 100% for all 57 specimens displaying the N501Y mutation, which were confirmed by Sanger sequencing to be typed as A23063T, including one specimen with mixed signal for wild type and mutant. Negative percent agreement was 100% in all 103 specimens typed as N501 wild type, with A23063 identified as wild type by Sanger sequencing. The identification of circulating SARS-CoV-2 lineages carrying an N501Y mutation is critical for surveillance purposes. Current identification methods rely primarily on Sanger sequencing or whole-genome sequencing, which are time consuming, labor intensive, and costly. The assay described herein is an efficient tool for high-volume specimen screening for SARS-CoV-2 VOCs and for selecting specimens for confirmatory Sanger or whole-genome sequencing. IMPORTANCE During the coronavirus disease 2019 (COVID-19) pandemic, several variants of concern (VOCs) have been detected, for example, B.1.1.7, B.1.351, P.1, and B.1.617.2. The VOCs pose a threat to public health efforts to control the spread of the virus. As such, surveillance and monitoring of these VOCs is of the utmost importance. Our real-time RT-PCR assay helps with surveillance by providing an easy method to quickly survey SARS-CoV-2 specimens for VOCs carrying the N501Y single nucleotide polymorphism (SNP). Samples that test positive for the N501Y mutation in the spike gene with our assay can be sequenced to identify the lineage. Thus, our assay helps to focus surveillance efforts and decrease turnaround times.

Impact of coronavirus disease 2019 (COVID-19) pre-test probability on positive predictive value of high cycle threshold severe acute respiratory coronavirus virus 2 (SARS-CoV-2) real-time reverse transcription polymerase chain reaction (RT-PCR) test results.

OBJECTIVES: Performance characteristics of SARS-CoV-2 nucleic acid detection assays are understudied within contexts of low pre-test probability, including screening asymptomatic persons without epidemiological links to confirmed cases, or asymptomatic surveillance testing. SARS-CoV-2 detection without symptoms may represent presymptomatic or asymptomatic infection, resolved infection with persistent RNA shedding, or a false-positive test. This study assessed the positive predictive value of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) assays by retesting positive specimens from 5 pre-test probability groups ranging from high to low with an alternate assay. METHODS: In total, 122 rRT-PCR positive specimens collected from unique patients between March and July 2020 were retested using a laboratory-developed nested RT-PCR assay targeting the RNA-dependent RNA polymerase (RdRp) gene followed by Sanger sequencing. RESULTS: Significantly fewer (15.6%) positive results in the lowest pre-test probability group (facilities with institution-wide screening having ≤3 positive asymptomatic cases) were reproduced with the nested RdRp gene RT-PCR assay than in each of the 4 groups with higher pre-test probability (individual group range, 50.0%-85.0%). CONCLUSIONS: Large-scale SARS-CoV-2 screening testing initiatives among low pre-test probability populations should be evaluated thoroughly prior to implementation given the risk of false-positive results and consequent potential for harm at the individual and population level.

One swab, two tests: Validation of dual SARS-CoV-2 testing on the Abbott ID NOW™.

BACKGROUND: Point-of-care tests (POCT) are promising tools to detect SARS-CoV-2 in specific settings. Initial reports suggest the ID NOW™ COVID-19 assay (Abbott Diagnostics Inc, USA) is less sensitive than standard real-time reverse transcription polymerase chain reaction (rRT-PCR) assays. This has raised concern over false negatives in SARS-CoV-2 POCT. OBJECTIVES: We compared the performance of the ID NOW™ COVID-19 assay to our in-house rRT-PCR assay to assess whether dry swabs used in ID NOW™ testing could be stored in transport media and be re-tested by rRT-PCR for redundancy and to provide material for further investigation. METHODS: Paired respiratory swabs collected from patients at three acute care hospitals were used. One swab in transport media (McMaster Molecular Media (MMM)) was tested for SARS-CoV-2 by a laboratory-developed two-target rRT-PCR assay. The second was stored dry in a sterile container and tested by the ID NOW™ COVID-19 assay. Following ID NOW™ testing, dry swabs were stored in MMM for up to 48 h and re-tested by rRT-PCR. Serially diluted SARS-CoV-2 particles were used to assess the impact of heat inactivation and storage time. RESULTS: Respiratory swabs (n = 343) from 179 individuals were included. Using rRT-PCR results as the comparator, the ID NOW™ COVID-19 assay had positive (PPA) and negative (NPA) percent agreements of 87.0% (95% CI:0.74-0.94) and 99.7% (95% CI:0.98-0.99). Re-tested swabs placed in MMM following ID NOW testing had PPA and NPA of 88.8% (95% CI:0.76-0.95) and 99.7% (95% CI:0.98-0.99), respectively. CONCLUSIONS: Storing spent dry swabs in transport media for redundancy rRT-PCR testing is a potential approach to address possible false negatives with the ID NOW™ COVID-19 assay.

Impact of Rejection of Low-Quality Wound Swabs on Antimicrobial Prescribing: A Controlled Before-After Study.

In this controlled before-after study, wound swabs were only processed for culture, identification, and susceptibility testing if a quality metric, determined by the Q score, was met. Rejection of low-quality wound swabs resulted in a modest decrease in reflexive antibiotic initiation while reducing laboratory workload and generating few clinician requests.

Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli.

The rising rates of antibiotic resistance increasingly compromise empirical treatment. Knowing the antibiotic susceptibility of a pathogen's close genetic relative(s) may improve empirical antibiotic selection. Using genomic and phenotypic data for Escherichia coli isolates from three separate clinically derived databases, we evaluated multiple genomic methods and statistical models for predicting antibiotic susceptibility, focusing on potentially rapidly available information, such as lineage or genetic distance from archived isolates. We applied these methods to derive and validate the prediction of antibiotic susceptibility to common antibiotics. We evaluated 968 separate episodes of suspected and confirmed infection with Escherichia coli from three geographically and temporally separated databases in Ontario, Canada, from 2010 to 2018. Across all approaches, model performance (area under the curve [AUC]) ranges for predicting antibiotic susceptibility were the greatest for ciprofloxacin (AUC, 0.76 to 0.97) and the lowest for trimethoprim-sulfamethoxazole (AUC, 0.51 to 0.80). When a model predicted that an isolate was susceptible, the resulting (posttest) probabilities of susceptibility were sufficient to warrant empirical therapy for most antibiotics (mean, 92%). An approach combining multiple models could permit the use of narrower-spectrum oral agents in 2 out of every 3 patients while maintaining high treatment adequacy (∼90%). Methods based on genetic relatedness to archived samples of E. coli could be used to predict antibiotic resistance and improve antibiotic selection.

2018 in review: five hot topics in tropical medicine.

The year 2018 heralded many new developments in the field of tropical medicine, including licensure of novel drugs for novel indications, licensure of existing drugs for existing indications but in novel settings, and globalized outbreaks of both vector-borne and zoonotic diseases. We herein describe five top stories in tropical medicine that occurred during 2018, and illuminate the practice-changing development within each story.