When the Trojan horse is unable to reach inside the city: investigation of the mechanism of resistance behind the first reported cefiderocol-resistant E. coli in Canada.

Gram-negative metallo-ß-lactamase-producing bacteria can be extremely problematic, especially when found to be extensively drug-resistant (XDR). Cefiderocol is a novel antimicrobial that has been shown to overcome most carbapenemases, with very rare resistance reported to date. Within our institution, two multidrug-resistant and one XDR strains were isolated from a patient who recently emigrated from India. Each isolate underwent whole-genome sequencing to resolve plasmids and determine phylogenetics, strain typing, and mechanisms of resistance. The XDR E. coli was ST167, harbored NDM-5, cirA and PBP3 mutations, consistent with cefiderocol resistance. Our study suggests that the NDM region is required in conjunction with cirA and PBP3 mutations. It is not clear why; however, our study did determine a potential novel iron-transport region unique to the cefiderocol-resistant isolate. This is the first characterized cefiderocol-resistant E.coli reported from Canada. Health centers should be on alert for this clone.IMPORTANCEThe development of cefiderocol, a novel siderophore cephalosporin, has provided additional options to the treatment of extensively drug-resistant (XDR) Gram-negative bacteria. Resistance to cefiderocol is poorly understood and only recently described. Here, we describe a case of a patient with recent travel to India harboring three Escherichia coli isolates, one resistant and two susceptible to cefiderocol. Two isolates are highly similar genetically, allowing the mechanism of resistance to be described more closely. The importance of this manuscript contributes both globally to the understanding of cefiderocol resistance in E. coli as well as nationally as this is the first resistant case reported in Canada. This is especially concerning as cefiderocol is not currently approved in Canada. The implications of reporting emerging resistance to new antimicrobials for XDR Gram negatives are impactful to infectious disease specialists, clinical microbiologists, physicians, and public health.

Sodium butyrate supresses malignant human mast cell proliferation, downregulates expression of KIT and promotes differentiation.

Sodium butyrate (NaBu) is a class I histone deacetylase inhibitor (HDACi) that can impede the proliferation of transformed cells. Although some HDACi downregulate the expression of the stem cell factor receptor (KIT/CD117), the effect of NaBu on KIT expression and human mast cell proliferation requires further elucidation. In this study, we examined the effects of NaBu on three transformed human mast cell lines, HMC-1.1, HMC-1.2 and LAD2. NaBu (100 µM) inhibited the proliferation and metabolic activity of all three cell lines without significantly affecting their viability, suggesting that although the cells had ceased to divide, they were not yet undergoing apoptosis. Cell cycle analysis using the cell-permeant dye, propidium iodide, indicated that NaBu significantly blocked the cell cycle progression of HMC-1.1 and HMC-1.2 from G1 to G2/M phases. Furthermore, NaBu downregulated the expression of C-KIT mRNA and KIT protein expression in all three cell lines, but this effect was most significant in the HMC-1.1 and HMC-1.2, both of which harbour activating mutations in KIT, which proliferate more rapidly than LAD2. These data support earlier observations showing that human mast cell lines are sensitive to histone deacetylase inhibition. However, our data presents the novel observation that inhibition of cell proliferation by NaBu was not associated with a loss in cell viability but rather an arrest of the cell cycle. Higher concentrations of NaBu led to modest increases in histamine content, tryptase expression, and granularity. In conclusion, NaBu treatment of human mast cell lines led to a modest enhancement of the hallmarks of mature mast cells.

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.

Respiratory virus coinfections with severe acute respiratory coronavirus virus 2 (SARS-CoV-2) continue to be rare one year into the coronavirus disease 2019 (COVID-19) pandemic in Alberta, Canada (June 2020-May 2021).

To assess the burden of respiratory virus coinfections with severe acute respiratory coronavirus virus 2 (SARS-CoV-2), this study reviewed 4,818 specimens positive for SARS-CoV-2 and tested using respiratory virus multiplex testing. Coinfections with SARS-CoV-2 were uncommon (2.8%), with enterovirus or rhinovirus as the most prevalent target (88.1%). Respiratory virus coinfection with SARS-CoV-2 remains low 1 year into the coronavirus disease 2019 (COVID-19) pandemic.

Alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity.

OBJECTIVES: The COVID-19 pandemic and ensuing public health emergency has emphasized the need to study SARS-CoV-2 pathogenesis. The human microbiome has been shown to regulate the host immune system and may influence host susceptibility to viral infection, as well as disease severity. Several studies have assessed whether compositional alterations in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection. However, the results of these studies were varied, and many did not account for disease severity. This study aims to examine whether compositional differences in the nasopharyngeal microbiota are associated with SARS-CoV-2 infection status and disease severity. METHODS: We performed Nanopore full-length 16S rRNA sequencing on 194 nasopharyngeal swab specimens from hospitalized and community-dwelling SARS-CoV-2-infected and uninfected individuals. Sequence data analysis was performed using the BugSeq 16S analysis pipeline. RESULTS: We found significant beta (PERMANOVA p < 0.05), but not alpha (Kruskal-Wallis p > 0.05) diversity differences in the nasopharyngeal microbiota among our study groups. We identified several differentially abundant taxa associated with SARS-CoV-2 infection status and disease severity using ALDEx2. Finally, we observed a trend towards higher abundance of Enterobacteriaceae in specimens from hospitalized SARS-CoV-2-infected patients. CONCLUSIONS: This study identified several alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity. Understanding the role of the microbiome in infection susceptibility and severity may open new avenues of research for disease prevention and treatment.

BugSplit enables genome-resolved metagenomics through highly accurate taxonomic binning of metagenomic assemblies.

A large gap remains between sequencing a microbial community and characterizing all of the organisms inside of it. Here we develop a novel method to taxonomically bin metagenomic assemblies through alignment of contigs against a reference database. We show that this workflow, BugSplit, bins metagenome-assembled contigs to species with a 33% absolute improvement in F1-score when compared to alternative tools. We perform nanopore mNGS on patients with COVID-19, and using a reference database predating COVID-19, demonstrate that BugSplit's taxonomic binning enables sensitive and specific detection of a novel coronavirus not possible with other approaches. When applied to nanopore mNGS data from cases of Klebsiella pneumoniae and Neisseria gonorrhoeae infection, BugSplit's taxonomic binning accurately separates pathogen sequences from those of the host and microbiota, and unlocks the possibility of sequence typing, in silico serotyping, and antimicrobial resistance prediction of each organism within a sample. BugSplit is available at https://bugseq.com/academic .

Ten Years of Diphtheria Toxin Testing and Toxigenic Cutaneous Diphtheria Investigations in Alberta, Canada: A Highly Vaccinated Population.

BACKGROUND: Respiratory diphtheria is a potentially fatal toxin-mediated disease that is rare among highly vaccinated populations. Cutaneous infections with toxigenic Corynebacterium diphtheriae are most commonly linked to travel to an endemic region. Corynebacterium ulcerans has emerged as a predominant, locally acquired cause of respiratory and cutaneous diphtheria in Western Europe. Recently, public health agencies from several highly vaccinated regions expanded their guidelines to investigate toxigenic cutaneous diphtheria regardless of travel history. With relatively unknown epidemiology of C diphtheriae in North America, and increasing diphtheria toxin testing over the last decade, this change could lead to substantial increases in public health investigations with unclear benefits. METHODS: This study examined the diagnostic and public health benefits of toxigenic cutaneous diphtheria investigations in the highly vaccinated population of Alberta, Canada, where travel history is not required for cutaneous diphtheria investigations. All C diphtheriae isolates collected between 2010 and 2019 were reviewed for specimen source, toxigenicity, biovar, and associated clinical and public health data. RESULTS: Of these, 5% of C diphtheriae isolates were toxigenic and 82% were isolated from cutaneous sites. Three cases of toxigenic cutaneous disease were identified, none from patients with recent travel. Contact tracing identified asymptomatic C diphtheriae colonization among 0%-26% of close contacts, with identical isolate profiles among colonized contacts and primary cases. CONCLUSIONS: Cutaneous diphtheria in nonendemic regions warrants public health investigation regardless of travel history and overall vaccination levels. This study underscores the importance of including C ulcerans in public health guidelines to assess the overall prevalence and epidemiology of toxigenic corynebacteria.

Decline of Influenza and Respiratory Viruses With COVID-19 Public Health Measures: Alberta, Canada.

OBJECTIVE: To determine the incidence of influenza and noninfluenza respiratory viruses (NIRVs) pre-/post-implementation of public health measures aimed to decrease coronavirus disease 2019 (COVID-19) transmission using population-based surveillance data. We hypothesized that such measures could reduce the burden of respiratory viruses (RVs) transmitting via the same routes. PATIENTS AND METHODS: An interrupted time-series analysis of RV surveillance data in Alberta, Canada, from May 2017 to July 2020 was conducted. The burden of influenza and NIRVs before and after intervention initiation at week 11 was compared. The analysis was adjusted for seasonality, overdispersion, and autocorrelation. RESULTS: During the study period, an average of 708 and 4056 weekly respiratory multiplex molecular panels were conducted pre-/post-intervention, respectively. We found significant reductions in test positivity rates in the postintervention period for influenza (-94.3%; 95% CI, -93.8 to 97.4%; P<.001) and all NIRVs (-76.5%; 95% CI, -77.3 to -75.8%; P<.001) in the crude model, and -86.2% (95% CI, -91.5 to -77.4%: P<.001) and -75% (95% CI, -79.7 to -69.3%; P<.001), respectively, in the adjusted models. Subanalyses for individual viruses showed significant decreases in respiratory syncytial virus, human metapneumovirus, enterovirus/rhinovirus, and parainfluenza. For non-severe acute respiratory coronavirus 2 human coronaviruses, the decline was not statistically significant after adjustment (-22.3%; 95% CI, -49.3 to +19%, P=.246). CONCLUSION: The implementation of COVID-19 public health measures likely resulted in reduced transmission of common RVs. Although drastic lockdowns are unlikely to be required given widespread COVID-19 vaccination, targeted implementation of such measures can lower RV disease burden. Studies to evaluate relative contributions of individual interventions are warranted.

Nanopore metagenomic sequencing for detection and characterization of SARS-CoV-2 in clinical samples.

OBJECTIVES: The COVID-19 pandemic has underscored the need for rapid novel diagnostic strategies. Metagenomic Next-Generation Sequencing (mNGS) may allow for the detection of pathogens that can be missed in targeted assays. The goal of this study was to assess the performance of nanopore-based Sequence-Independent Single Primer Amplification (SISPA) for the detection and characterization of SARS-CoV-2. METHODS: We performed mNGS on clinical samples and designed a diagnostic classifier that corrects for barcode crosstalk between specimens. Phylogenetic analysis was performed on genome assemblies. RESULTS: Our assay yielded 100% specificity overall and 95.2% sensitivity for specimens with a RT-PCR cycle threshold value less than 30. We assembled 10 complete, and one near-complete genomes from 20 specimens that were classified as positive by mNGS. Phylogenetic analysis revealed that 10/11 specimens from British Columbia had a closest relative to another British Columbian specimen. We found 100% concordance between phylogenetic lineage assignment and Variant of Concern (VOC) PCR results. Our assay was able to distinguish between the Alpha and Gamma variants, which was not possible with the current standard VOC PCR being used in British Columbia. CONCLUSIONS: This study supports future work examining the broader feasibility of nanopore mNGS as a diagnostic strategy for the detection and characterization of viral pathogens.

Stability of SARS-CoV-2 IgG in multiple laboratory conditions and blood sample types.

BACKGROUND: COVID-19 seroprevalence studies use serum/plasma samples to detect SARS-CoV-2 IgG. Data supporting alternate specimen types and freeze-thaw antibody stability is lacking. The stability of IgG and other immunoglobulins in multiple blood sample types stored in differing conditions and multiple freeze-thaw cycles (FTCs) was evaluated. MATERIALS AND METHODS: Serum, plasma, and heparinized-plasma samples were collected from COVID-19 recovered individuals. Samples underwent testing for SARS-CoV-2 antibodies upon collection, after each of 10-12 FTCs, and storage at -70°C, -20°C, 4°C, and room-temperature for 10-12 days using four high-throughput commercial assays, two rapid-test cassettes, a manual ELISA, and a surrogate neutralization assay. RESULTS: All three specimen types were collected from 34 COVID-19 recovered seropositive individuals (≥21 days post-symptoms). Using the Architect and Liaison assays, a positive qualitative SARS-CoV-2 IgG result was detected daily up to 12 FTCs and up to 10 days of storage at different temperatures. An additional 25 plasma samples consistently demonstrated detection of SARS-CoV-2 antibodies daily after 12 FTCs and storage at -20°C using two rapid test cassette assays (SD Biosensor and Hangzhou All Test), manual (Beijing Wantai) and surrogate neutralization (GenScript) ELISAs, and two high-throughput assays (Roche Elecsys nucleocapsid and spike). IgM antibodies were less frequently detected by one of the rapid test cassette assays. CONCLUSIONS: Serum, plasma, and heparinized-plasma constitute reliable samples for SARS-CoV-2 antibody detection. In particular, the IgG response was stable and reliably detected after multiple FTCs and storage at common laboratory conditions. IgM detection was variable due to the labile nature of this antibody class.

Epidemiological and Clinical Characteristics of Alveolar Echinococcosis: An Emerging Infectious Disease in Alberta, Canada.

Human alveolar echinococcosis (AE) is a zoonotic cestode infection which is usually fatal in the absence of treatment. Treatment involves major surgery or indefinite antiparasitic therapy. The incidence is rising in Europe and Asia, with an increased risk observed in immunocompromised individuals. Previously, AE acquisition in North America was extremely rare, except for one remote Alaskan Island. Recent studies have demonstrated a new European-like strain of Echinococcus multilocularis (Em) in wildlife and in human AE in western Canada. We report the experience of all AE patients diagnosed in Alberta. Each was diagnosed by histopathology, serology, and PCR-confirmed by a reference laboratory. Seventeen cases of human AE, aged 19-78 years, nine females, were diagnosed between 2013 and 2020: all definitely or probably acquired in Alberta. Six lived in urban areas, and 14 had kept dogs. In eight, the lesions were found incidentally on abdominal imaging performed for other indications. Six were immunocompromised to varying degrees. Six were first diagnosed at surgery. All have been recommended benzimidazole therapy. One died of surgical complications. Clinicians should be aware of this diagnostic possibility in patients presenting with focal nonmalignant hepatic mass lesions. Greater urbanization of coyotes, the predominant definitive host of Em in Alberta, and growing numbers of immune suppressed individuals in the human population may lead to increasing recognition of AE in North America.

False negative rate of COVID-19 PCR testing: a discordant testing analysis.

BACKGROUND: COVID-19 is diagnosed via detection of SARS-CoV-2 RNA using real time reverse-transcriptase polymerase chain reaction (rtRT-PCR). Performance of many SARS-CoV-2 rtRT-PCR assays is not entirely known due to the lack of a gold standard. We sought to evaluate the false negative rate (FNR) and sensitivity of our laboratory-developed SARS-CoV-2 rtRT-PCR targeting the envelope (E) and RNA-dependent RNA-polymerase (RdRp) genes. METHODS: SARS-CoV-2 rtRT-PCR results at the Public Health Laboratory (Alberta, Canada) from January 21 to April 18, 2020 were reviewed to identify patients with an initial negative rtRT-PCR followed by a positive result on repeat testing within 14 days (defined as discordant results). Negative samples from these discordant specimens were re-tested using three alternate rtRT-PCR assays (targeting the E gene and N1/N2 regions of the nucleocapsid genes) to assess for false negative (FN) results. RESULTS: During the time period specified, 95,919 patients (100,001 samples) were tested for SARS-CoV-2. Of these, 49 patients were found to have discordant results including 49 positive and 52 negative swabs. Repeat testing of 52 negative swabs found five FNs (from five separate patients). Assuming 100% specificity of the diagnostic assay, the FNR and sensitivity in this group of patients with discordant testing was 9.3% (95% CI 1.5-17.0%) and 90.7% (95% CI 82.6-98.9%) respectively. CONCLUSIONS: Studies to understand the FNR of routinely used assays are important to confirm adequate clinical performance. In this study, most FN results were due to low amounts of SARS-CoV-2 virus concentrations in patients with multiple specimens collected during different stages of infection. Post-test clinical evaluation of each patient is advised to ensure that rtRT-PCR results are not the only factor in excluding COVID-19.

Donor Graft Cytomegalovirus Serostatus and the Risk of Arterial and Venous Thrombotic Events in Seronegative Recipients After Non-Thoracic Solid Organ Transplantation.

BACKGROUND: Cytomegalovirus (CMV) is the most common opportunistic pathogen, following solid organ transplantation (SOT), that leads to direct and indirect effects. The aim of this study was to assess the impact of CMV exposure at transplantation on the rate of posttransplant thrombotic events (TEs). METHODS: We conducted a retrospective cohort study of patients transplanted at the University of Alberta Hospital between July 2005 and January 2018. We included adult SOT CMV-seronegative recipients at transplantation who received an allograft from either a seropositive donor (D+/R-) or a seronegative donor (D-/R-). RESULTS: A total of 392 SOT recipients were included: 151 (39%) liver, 188 (48%) kidney, 45 (11%) pancreas, and 8 (2%) other transplants. The mean age was 47 years, 297 (76%) were males, and 181 (46%) had a CMV D+/R- donor. Patients in the CMV D+/R- cohort were slightly older (51 years versus 48 years in the D-/R- cohort; P = .036), while other variables, including cardiovascular risk factors and pretransplant TEs, were not different between groups. Overall, TEs occurred in 35 (19%) patients in the CMV D+/R- group, versus 21 (10%) in the CMV D-/R- group, at 5 years of follow-up (P = .008); the incidence rates per 100 transplant months were 5.12 and 1.02 in the CMV D+/R- and CMV D-/R- groups, respectively (P = .003). After adjusting for potential confounders with a Cox regression model, a CMV D+/R- transplantation was independently associated with an increased risk of a TE over 5 years (adjusted hazard ratio, 3.027; 95% confidence interval, 1.669-5.488). CONCLUSIONS: A CMV D+/R- transplantation is associated with an increased risk of a TE posttransplantation.

Evaluation of Six Commercial Mid- to High-Volume Antibody and Six Point-of-Care Lateral Flow Assays for Detection of SARS-CoV-2 Antibodies.

Coronavirus disease (COVID) serological tests are essential to determine the overall seroprevalence of a population and to facilitate exposure estimates within that population. We performed a head-to-head assessment of enzyme immunoassays (EIAs) and point-of-care lateral flow assays (POCTs) to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies. Demographics, symptoms, comorbidities, treatment, and mortality of patients whose sera were used were also reviewed. Six EIAs (Abbott, Affinity, Bio-Rad, DiaSorin, Euroimmun, and Roche) and six POCTs (BTNX, Biolidics, Deep Blue, Genrui, Getein BioTech, and Innovita) were evaluated for the detection of SARS-CoV-2 antibodies in known COVID-19-infected individuals. Sensitivity of EIAs ranged from 50 to 100%, with only four assays having overall sensitivities of >95% after 21 days after symptom onset. Notably, cross-reactivity with other respiratory viruses (parainfluenza virus [PIV-4] [n = 5], human metapneumovirus [hMPV] [n = 3], rhinovirus/enterovirus [n = 1], CoV-229E [n = 2], CoV-NL63 [n = 2], and CoV-OC43 [n = 2]) was observed; however, overall specificity of EIAs was good (92 to 100%; all but one assay had specificity above 95%). POCTs were 0 to 100% sensitive >21 days after onset, with specificity ranging from 96 to 100%. However, many POCTs had faint banding and were often difficult to interpret. Serology assays can detect SARS-CoV-2 antibodies as early as 10 days after symptom onset. Serology assays vary in their sensitivity based on the marker (IgA/IgM versus IgG versus total) and by manufacturer; however, overall only 4 EIAs and 4 POCTs had sensitivities of >95% >21 days after symptom onset. Cross-reactivity with other seasonal coronaviruses is of concern. Serology assays should not be used for the diagnosis of acute infection but rather in carefully designed serosurveys to facilitate understanding of seroprevalence in a population and to identify previous exposure to SARS-CoV-2.

When medicine transforms art.

A 40-year-old female with a history of type 1 diabetes mellitus and solitary pancreas transplant, presented with pancreatic graft rejection 1-year post-transplant. Incidentally, a 1.1 cm right lower lobe cavity was identified during her workup. Given the augmentation of immunosuppression, voriconazole was empirically started for possible invasive pulmonary aspergillosis. As the patient was a painter, this resulted in a significant change in the colors of her paintings. Ultimately, she was diagnosed with pulmonary coccidioidomycosis and her visual disturbances resolved after the voriconazole was changed to fluconazole. Voriconazole causes visual disturbances in 20%-30% of the patients most commonly phototopsias; dyschromatopsias typically involving the tritan axis have also been reported. This case illustrates well the potential impact of voriconazole on spectral sensitivity and color perception.

The Novel Receptor C5aR2 Is Required for C5a-Mediated Human Mast Cell Adhesion, Migration, and Proinflammatory Mediator Production.

C5a generated during complement activation possesses proinflammatory and immunoregulatory properties critical for the development and modulation of allergic immune responses. In immune cells, C5a mediates its effects through binding to two G protein-coupled receptors, C5aR1 and C5aR2. Mast cells are key effectors in allergic reactions, and decades of research have suggested that the majority of C5a effects on mast cells are mediated through C5aR1, whereas the expression and function of C5aR2 have not been explored. We demonstrated that the human mast cell line Laboratory of Allergic Diseases 2 (LAD2) expresses surface C5aR2 but not C5aR1, whereas CD34(+) cell-derived primary mast cells do not express surface C5aR1 or C5aR2. Stem cell factor and IL-4 upregulated C5aR2 expression on LAD2 cells. Furthermore, C5a caused internalization of LAD2 cell-surface C5aR2. We therefore used LAD2 cells as a model to study C5a/C5aR2-induced biological responses and signaling in human mast cells. We found that whereas C5a was unable to induce degranulation, it stimulated GM-CSF, TNF, CXCL10, and CCL2 production. C5a caused ERK phosphorylation, a signaling molecule important in cytokine and chemokine generation. In addition, C5a stimulated adhesion and chemotaxis of mast cells. Wortmannin, an inhibitor of PI3K, and small interfering RNA against ß-arrestin-2 blocked C5a-induced adhesion. Silencing of C5aR2 using lentiviral short hairpin RNA rendered the cells unresponsive to C5a-induced adhesion, chemotaxis, and mediator release, as well as ERK phosphorylation. Overall, this study reveals a novel role for C5aR2 in C5a-mediated activation of mast cells and demonstrates that C5aR2 ligation initiates a ß-arrestin-2-, PI3K-, and ERK-dependent signaling pathway in these cells.