Automated detection of methicillin-resistant Staphylococcus aureus with the MRSA CHROM imaging application on BD Kiestra Total Lab Automation System.

The virulence of methicillin-resistant Staphylococcus aureus (MRSA) and its potentially fatal outcome necessitate rapid and accurate detection of patients colonized with MRSA in healthcare settings. Using the BD Kiestra Total Lab Automation (TLA) System in conjunction with the MRSA Application (MRSA App), an imaging application that uses artificial intelligence to interpret colorimetric information (mauve-colored colonies) indicative of MRSA pathogen presence on CHROMagar chromogenic media, anterior nares specimens from three sites were evaluated for the presence of mauve-colored colonies. Results obtained with the MRSA App were compared to manual reading of agar plate images by proficient laboratory technologists. Of 1,593 specimens evaluated, 1,545 (96.98%) were concordant between MRSA App and laboratory technologist reading for the detection of MRSA growth [sensitivity 98.15% (95% CI, 96.03, 99.32) and specificity 96.69% (95% CI, 95.55, 97.60)]. This multi-site study is the first evaluation of the MRSA App in conjunction with the BD Kiestra TLA System. Using the MRSA App, our results showed 98.15% sensitivity and 96.69% specificity for the detection of MRSA from anterior nares specimens. The MRSA App, used in conjunction with laboratory automation, provides an opportunity to improve laboratory efficiency by reducing laboratory technologists' labor associated with the review and interpretation of cultures.

Spatiotemporal trends and socioecological factors associated with Lyme disease in eastern Ontario, Canada from 2010-2017.

Currently, there is limited knowledge about socioeconomic, neighbourhood, and local ecological factors that contribute to the growing Lyme disease incidence in the province of Ontario, Canada. In this study, we sought to identify these factors that play an important role at the local scale, where people are encountering ticks in their communities. We used reported human Lyme disease case data and tick surveillance data submitted by the public from 2010-2017 to analyze trends in tick exposure, spatiotemporal clusters of infection using the spatial scan statistic and Local Moran's I statistic, and socioecological risk factors for Lyme disease using a multivariable negative binomial regression model. Data were analyzed at the smallest geographic unit, consisting of 400-700 individuals, for which census data are disseminated in Canada. We found significant heterogeneity in tick exposure patterns based on location of residence, with 65.2% of Lyme disease patients from the city of Ottawa reporting tick exposures outside their health unit of residence, compared to 86.1%-98.1% of patients from other, largely rural, health units, reporting peri-domestic exposures. We detected eight spatiotemporal clusters of human Lyme disease incidence in eastern Ontario, overlapping with three clusters of Borrelia burgdorferi-infected ticks. When adjusting for population counts, Lyme disease case counts increased with larger numbers of Borrelia burgdorferi-infected ticks submitted by the public, higher proportion of treed landcover, lower neighbourhood walkability due to fewer intersections, dwellings, and points of interest, as well as with regions of higher residential instability and lower ethnic concentration (Relative Risk [RR] = 1.25, 1.02, 0.67-0.04, 1.34, and 0.57, respectively, p < .0001). Our study shows that there are regional differences in tick exposure patterns in eastern Ontario and that multiple socioecological factors contribute to Lyme disease risk in this region.

Derivation and Internal Validation of a Model to Predict the Probability of Severe Acute Respiratory Syndrome Coronavirus-2 Infection in Community People.

BACKGROUND: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease. There are concerns regarding limited testing capacity and the exclusion of cases from unproven screening criteria. Knowing COVID-19 risks can inform testing. This study derived and assessed a model to predict risk of SARS-CoV-2 in community-based people. METHODS: All people presenting to a community-based COVID-19 screening center answered questions regarding symptoms, possible exposure, travel, and occupation. These data were anonymously linked to SARS-CoV-2 testing results. Logistic regression was used to derive a model to predict SARS-CoV-2 infection. Bootstrap sampling evaluated the model. RESULTS: A total of 9172 consecutive people were studied. Overall infection rate was 6.2% but this varied during the study period. SARS-CoV-2 infection likelihood was primarily influenced by contact with a COVID-19 case, fever symptoms, and recent case detection rates. Internal validation found that the SARS-CoV-2 Risk Prediction Score (SCRiPS) performed well with good discrimination (c-statistic 0.736, 95%CI 0.715-0.757) and very good calibration (integrated calibration index 0.0083, 95%CI 0.0048-0.0131). Focusing testing on people whose expected SARS-CoV-2 risk equaled or exceeded the recent case detection rate would increase the number of identified SARS-CoV-2 cases by 63.1% (95%CI 54.5-72.3). CONCLUSION: The SCRiPS model accurately estimates the risk of SARS-CoV-2 infection in community-based people undergoing testing. Using SCRiPS can importantly increase SARS-CoV-2 infection identification when testing capacity is limited.

Arthroscopic removal of osteochondral fragments in the dorsal pouch of the proximal intertarsal joint in 29 horses.

OBJECTIVE: To describe the radiographic and surgical findings of horses with osteochondral fragments (OCF) in the proximal intertarsal joint (PIJ) and to detail the technique for arthroscopic fragment retrieval and report outcomes. STUDY DESIGN: Retrospective case series. ANIMALS: Twenty-nine horses (32 tarsi) with OCF in the PIJ. METHODS: Medical records of horses with radiographic evidence of OCF in the PIJ were reviewed. Clinical features, number of fragments, location, arthroscopic appearance, and outcome were recorded. Technical modifications with visual aids specific to this arthroscopic technique are described. RESULTS: Twenty-seven horses (93%) had radiographic evidence of osteochondritis dissecans lesions in the tarsocrural joint (TCJ). OCF were most commonly located distal to the medial trochlear ridge of the talus. In all cases, fragments were successfully retrieved with a technique based on exposing the fragments after resection of the proximal intertarsal joint capsule (PIJC). Fragments were visible from the TCJ prior resection of the PIJC in 4 of 32 tarsi. A third portal was created to access fragments located distal to the lateral trochlear ridge in 3 of 32 tarsi. Moderate intra-articular bleeding occurred when the PIJC was resected in 3 of 32 tarsi. One horse had postoperative swelling that resolved with conservative medical management. All horses with long-term follow-up available (16/29) started training or returned to their athletic career. CONCLUSION AND CLINICAL SIGNIFICANCE: The arthroscopic technique based on resection of PIJC was effective in retrieving OCF in the PIJ and was associated with minor complications. The clinical relevance of these fragments in the PIJ remains unknown.

Characterization of an Enterococcus gallinarum Isolate Carrying a Dual vanA and vanB Cassette.

The ability of vancomycin resistance determinants to be horizontally transferred within enterococci species is a concern. Identification and characterization of vancomycin-resistant enterococci (VRE) in a clinical isolate have a significant impact on infection control practices. In this study, we describe a clinical isolate of Enterococcus gallinarum exhibiting high-level resistance to vancomycin and teicoplanin. The genetic characterization of this isolate showed the presence of vanA and vanB genes in addition to the naturally carried vanC gene. vanA was identified on pA6981, a 35,608-bp circular plasmid with significant homology to plasmid pS177. The vanB operon was integrated into the bacterial chromosome and showed a high level of homology to previously reported Tn1549 and Tn5382. To the best of our knowledge, this is the first report of E. gallinarum carrying both vanA and vanB operons, indicating the importance of identifying the vancomycin resistance mechanism in non-E. faecium and non-E. faecalis enterococcal species.

Competency assessment of microbiology medical laboratory technologists in Ontario, Canada.

Accreditation in Ontario, Canada, requires that licensed clinical laboratories participate in external quality assessment (also known as proficiency testing) and perform competency evaluation of their staff. To assess the extent of ongoing competency assessment practices, the Quality Management Program--Laboratory Services (QMP-LS) Microbiology Committee surveyed all 112 licensed Ontario microbiology laboratories. The questionnaire consisted of a total of 21 questions that included yes/no, multiple-choice, and short-answer formats. Participants were asked to provide information about existing programs, the frequency of testing, what areas are evaluated, and how results are communicated to the staff. Of the 111 responding laboratories, 6 indicated they did not have a formal evaluation program since they perform only limited bacteriology testing. Of the remaining 105 respondents, 87% perform evaluations at least annually or every 2 years, and 61% include any test or task performed, whereas 16% and 10% focus only on problem areas and high-volume complex tasks, respectively. The most common methods of evaluation were review of external quality assessment (EQA) challenges, direct observation, and worksheet review. With the exception of one participant, all communicate results to staff, and most take remedial action to correct the deficiencies. Although most accredited laboratories have a program to assess the ongoing competency of their staff, the methods used are not standardized or consistently applied, indicating that there is room for improvement. The survey successfully highlighted potential areas for improvement and allowed the QMP-LS Microbiology Committee to provide guidance to Ontario laboratories for establishing or improving existing microbiology-specific competency assessment programs.

Derivation and internal validation of the multivariate toxigenic C. difficile diarrhea model and risk score for emergency room and hospitalized patients with diarrhea.

Background: Many factors have been associated with the risk of toxigenic C. difficile diarrhea (TCdD). This study derived and internally validated a multivariate model for estimating the risk of TCdD in patients with diarrhea using readily available clinical factors. Methods: A random sample of 3,050 symptomatic emergency department or hospitalized patients undergoing testing for toxigenic C. difficile at a single teaching hospital between 2014 and 2018 was created. Unformed stool samples positive for both glutamate dehydrogenase antigen by enzyme immunoassay and tcdB gene by polymerase chain reaction were classified as TCdD positive. The TCdD Model was created using logistic regression and was modified to the TCdD Risk Score to facilitate its use. Results: 8.1% of patients were TCdD positive. TCdD risk increased with abdominal pain (adjusted odds ratio 1.3; 95% CI, 1.0-1.8), previous C. difficile diarrhea (2.5, 1.1-6.1), and prior antibiotic exposure, especially when sampled in the emergency department (4.2, 2.5-7.0) versus the hospital (1.7, 1.3-2.3). TCdD risk also increased when testing occurred earlier during the hospitalization encounter, when age and white cell count increased concurrently, and with decreased eosinophil count. In internal validation, the TCdD Model had moderate discrimination (optimism-corrected C-statistic 0.65, 0.62-0.68) and good calibration (optimism-corrected Integrated Calibration Index [ICI] 0.017, 0.001-0.022). Performance decreased slightly for the TCdD Risk Score (C-statistic 0.63, 0.62-0.63; ICI 0.038, 0.004-0.038). Conclusions: TCdD risk can be predicted using readily available clinical risk factors with modest accuracy.

Changes in fluoroquinolone resistance over 5 years (CANWARD 2007-11) in bacterial pathogens isolated in Canadian hospitals.

OBJECTIVES: The purpose of this study was to analyse Canadian national surveillance data, specifically fluoroquinolone resistance, from 2007 to 2011 inclusive, to determine trends in resistance over time and to assess correlations with patient demographic factors. METHODS: All isolates of Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas aeruginosa, Staphylococcus aureus and Streptococcus pneumoniae collected by the 10 sites that participated in the annual CANWARD surveillance studies in each of the 5 years were included in this analysis. A multifactorial logistic regression model was used to determine the variables with significant impact on fluoroquinolone resistance. RESULTS: The proportion of E. coli isolates resistant to ciprofloxacin increased significantly (P = 0.0005) between 2007 (20.0%) and 2011 (29.2%), although similar increases were not seen in K. pneumoniae, E. cloacae, P. aeruginosa and S. pneumoniae (tested against levofloxacin) (P > 0.05). Among isolates of S. aureus, there was a significant decrease in ciprofloxacin resistance from 34.4% in 2007 to 24.6% in 2011 (P < 0.0001). Resistance to ciprofloxacin was a component of most multidrug-resistant (MDR) phenotypes for E. coli, K. pneumoniae, E. cloacae, P. aeruginosa and S. aureus. CONCLUSIONS: A significant increase in the percentage of ciprofloxacin-resistant E. coli, primarily among urine isolates, and a significant decrease in the percentage of ciprofloxacin-resistant S. aureus occurred between 2007 and 2011. Notably, MDR isolates were frequently fluoroquinolone resistant for all organisms studied, except S. pneumoniae.

Leprosy-like illness in a patient with Mycobacterium lepromatosis from Ontario, Canada.

Here we present the first case of a patient from Ottawa Canada, presenting with leprosy-like illness associated with Mycobacterium lepromatosis. The patient had no history of travel to leprosy-endemic areas or any obvious risk factors. Clinically, the patient presented with an anesthetic maculopapular rash on the trunk, back, and extremities. A skin biopsy of a lesion revealed a dermal lymphohistiocytic infiltration involving the vessels with an inflammatory process extending to the nerves. A neurological exam also identified a severe sensorimotor polyneuropathy. Concurrently, the patient was diagnosed with non-resectable, non small cell carcinoma of the lung, further complicating his clinical presentation. A Kinyoun stain of nasal blows and a Fite stain of the skin biopsy revealed few to moderate acid fast bacilli respectively. Cultures of the skin biopsy and multiple nasal blows were negative. Molecular studies of a skin biopsy sample including sequence analysis of a 765 bp region of the 16s rRNA gene eventually identified the organism with 100% homology to M. lepromatosis. The patient was treated for leprosy and appeared to improve slightly on therapy but died as a result of his malignancy approximately five months after the initiation of therapy. This represents the first case of a patient with M. lepromatosis like illness outside of Mexico and Singapore.

Implementation of the Abbott ID Now COVID-19 assay at a tertiary care center: a prospective pragmatic implementation study during the third wave of SARS-CoV-2 in Ontario.

The Abbott ID Now COVID-19 assay is a point-of-care molecular diagnostic tool for the detection of SARS-CoV-2. We prospectively monitored implementation of the assay in a tertiary care hospital emergency department (ED) for the diagnosis of early symptomatic patients. A total of 269 paired nasopharyngeal swabs were tested in parallel with the ID Now and laboratory-based molecular methodologies, 191 of which met selection criteria for testing based on symptoms description and duration. Forty-six and 48 samples were positive for SARS-CoV-2 with the ID Now and reference molecular assays respectively. Percent positive and negative agreement were high (93.8% and 99.6% respectively), as were the sensitivity and specificity (93.8% and 99.5%). ID Now results were available 17.47 hours earlier than qRT-PCR. In symptomatic patients seen in ED within 7 to 10 days of symptoms onset, the ID Now COVID-19 assay allows for rapid and accurate detection of infection.

Effect of delayed entry of blood culture bottles in BACTEC automated blood culture system in the context of laboratory consolidation.

Delayed entry of blood culture bottles is frequent in consolidated laboratories. A retrospective study evaluated time from insertion to detection and total detection time as a function of preincubation time, and we prospectively looked for false negative results. 69,604 blood culture bottles were reviewed for preincubation time, incubation time and total detection time. Positive cultures for specific bacterial subtypes were reviewed to assess the effect of preincubation time on likelihood of detection. 492 negative blood cultures were prospectively tested by 16S RNA PCR and Staphylococcus-specific PCR for the presence of bacterial DNA. Mean preincubation time for samples collected within the city-limits was 3.94 h versus 9.49-18.89 h for other client sites. Higher preincubation times were partially mitigated by a lower incubation time, with an overall increase in total detection time. A lower odds ratio of recovery of Staphylococcus spp was identified, but not confirmed by terminal subcultures and molecular assays. Prolonged preincubation of blood cultures affects total detection time despite a reduction in incubation time. Successful centralization of microbiological services may depend upon optimization of courier routes for inoculated blood culture bottles. Our data supports consideration for an increase in suggested maximum preincubation times.

Evaluation of the Abbott PanbioTM COVID-19 Ag rapid antigen test for the detection of SARS-CoV-2 in asymptomatic Canadians.

Several rapid testing methodologies have been approved for testing of symptomatic individuals but have not been validated for asymptomatic screening. We evaluated performance of the Abbott PanbioTM COVID-19 rapid antigen assay in the asymptomatic setting. We conducted a prospective study in an urban assessment center and in the context of long-term care staff screening. A total of 3014 individuals submitted paired nasopharyngeal samples, which were tested in parallel with the rapid antigen and laboratory-based, RT-PCR assays SARS-CoV-2 detection. There was 54.5% concordance in positive results between the rapid antigen assay and RT-PCR. All positive rapid antigen assay results were confirmed by RT-PCR. The negative predictive value of the rapid antigen assay minimally improved on the negative pre-test probability of SARS-CoV-2 infection. The Abbott PanbioTM COVID-19 rapid antigen test allowed for faster identification of infected individuals but cannot be used to rule-out SARS-CoV-2 infection.

Temporal Dynamics and Evolution of SARS-CoV-2 Demonstrate the Necessity of Ongoing Viral Genome Sequencing in Ontario, Canada.

Genome-wide variation in SARS-CoV-2 reveals evolution and transmission dynamics which are critical considerations for disease control and prevention decisions. Here, we review estimates of the genome-wide viral mutation rates, summarize current COVID-19 case load in the province of Ontario, Canada (5 January 2021), and analyze published SARS-CoV-2 genomes from Ontario (collected prior to 24 November 2020) to test for more infectious genetic variants or lineages. The reported mutation rate (∼10-6 nucleotide [nt]-1 cycle-1) for SARS-CoV-2 is typical for coronaviruses. Analysis of published SARS-CoV-2 genomes revealed that the G614 spike protein mutation has dominated infections in Ontario and that SARS-CoV-2 lineages present in Ontario have not differed significantly in their rate of spread. These results suggest that the SARS-CoV-2 population circulating in Ontario has not changed significantly to date. However, ongoing genome monitoring is essential for identification of new variants and lineages that may contribute to increased viral transmission.

Ignatzschineria indica bacteremia in a patient with a maggot-infested heel ulcer: a case report and literature review.

An elderly patient was admitted with sepsis to a community hospital. The individual was found to have a foot wound infested with maggots, and clinical evidence of cellulitis. A blood culture was positive on day 2 with Ignatzschineria indica . The patient was treated successfully with a combination of antibiotics and manual removal of the maggots. Poor living conditions were central to his presentation.

Detection of plasmid-mediated KPC-producing Klebsiella pneumoniae in Ottawa, Canada: evidence of intrahospital transmission.

Klebsiella pneumoniae isolates from three patients admitted to the Ottawa Hospital, a 1,040-bed teaching hospital, were found to contain the plasmid-borne K. pneumoniae carbapenemase (KPC)-producing bla gene (bla(KPC)). There was evidence of person-to-person transmission for two patients. Screening of 186 clinical isolates revealed no additional bla(KPC)-containing isolates.

Shift in Epidemiology of Cryptococcal Infections in Ottawa with High Mortality in Non-HIV Immunocompromised Patients.

Cryptococcus neoformans is a fungus that can cause life-threatening infections. While human immunodeficiency virus (HIV)-positive status historically had the highest risk for cryptococcal infection and was associated with high mortality rates, there have been changes in HIV treatment and the epidemiology of other acquired immunodeficiencies, such as hematological malignancies. We conducted a retrospective case series analysis of patients who had cryptococcal infections documented at the Ottawa Hospital from 2005 to 2017. The Ottawa Hospital is a tertiary care hospital and provides complex care such as chemotherapy and transplantations. There were 28 confirmed cryptococcal infections. The most common underlying condition associated with cryptococcal infection was hematological malignancy (n = 8, 29%), followed by HIV (n = 5, 18%) and solid organ transplantation (n = 4, 14%). Furthermore, while there was a decrease in the number of cryptococcal infections in HIV patients after 2010 (four to one case), the number of cases in non-HIV immunocompromised patients increased from four in the years 2005-2010 to fourteen in 2011-2017. There were nine cryptococcal-attributable deaths. The case fatality rate was highest among patients with underlying hematological malignancies (63%), followed by solid organ transplant (50%) and HIV patients (20%). In conclusion, this study showed that there may be an epidemiological shift of cryptococcal infection in Ottawa. Additionally, infections may be associated with a worse prognosis in patients with a hematological malignancy and solid organ transplant than in patients with HIV infection in the modern era. Better prevention and/or treatment is warranted for high-risk populations.

A comparison of the Quidel Solana GAS assay, the Luminex Aries Group A Strep assay and the Focus Diagnostics Simplexa Group A Strep Direct assay for detection of Group A Streptococcus in throat swab specimens.

We compared three commercially available group A Streptococcus (GAS) nucleic acid amplification tests, the Quidel Solana GAS assay, the Luminex Aries Group A Strep assay and the Focus Diagnostics Simplexa Group A Strep Direct assay, with GAS bacterial culture. A true positive result was defined as one positive by culture or positive by ≥2/3 molecular methods. Two hundred eighty-seven throat swabs (207 children, 80 adults) were collected. The sensitivity of culture was 84.8% (95% CI 77.7-90.3%) with a specificity of 100% (95% CI 97.5-100%). The Solana assay sensitivity was 94.2% (95% CI 88.9-97.5%) with a specificity of 98.7% (95% CI 95.2-99.8%). Simplexa assay sensitivity was 99.3% (95% CI 96.0-99.9%) with a specificity of 95.3% (95% CI 90.6-98.1%). Aries assay sensitivity was 96.4% (95% CI 91.8-98.8%) with a specificity of 98.0% (95% CI 94.2-99.6%). In summary, all the molecular methods evaluated showed high sensitivity and specificity and were more sensitive than culture.

A comparison of the Quidel Solana HSV 1 + 2/VZV Assay, the Focus Diagnostics Simplexa HSV 1 & 2 Direct Assay and the Luminex Aries HSV 1&2 Assay for detection of herpes simplex virus 1 and 2 from swab specimens.

BACKGROUND: Molecular methods enable more rapid and sensitive detection of herpes simplex virus (HSV) than viral culture. OBJECTIVE: Three commercial molecular methods, all of which detect both HSV-1 and HSV-2, were compared to viral culture for the detection of HSV from swab specimens. STUDY DESIGN: Pediatric and adult patient viral swab specimens were cultured for HSV. Residual swab fluid was frozen at -80 °C until tested with the 3 molecular methods: the Quidel Solana HSV 1 + 2/VZV Assay, the Focus Diagnostics Simplexa HSV 1 & 2 Direct Assay and the Luminex Aries HSV 1&2 Assay. A true positive was defined as positive by culture or positive by ≥ 2/3 molecular methods. RESULTS: 177 specimens were studied. The sensitivity of culture was 81.3% (61/75, 95% CI 70.7-89.4%) and specificity was 100% (102/102, 95% CI 96.4-100%). The sensitivities of both the Solana and Simplexa were 100% (75/75, 95% CI 95.2-100%) and specificities were also both 100% (102/102, 95% CI 96.4-100%). The Aries had a sensitivity of 98.7% (74/75, 95% CI 92.8-99.97%) and specificity 99.0% (101/102, 95% CI 94.7-99.98%). All three molecular methods were significantly more sensitive than culture (p ≤ 0.0005 for Solana and Simplexa and p ≤ 0.0012 for Aries). CONCLUSION: All the molecular methods studied provided a significantly higher sensitivity than culture. In addition, the molecular methods took 1-2 hours to perform compared to a mean of 2.1 days for culture results. Use of any of the three molecular methods could lead to improved patient care.

Central venous catheter-associated Leifsonia aquatica bacteremia in a hemodialysis-dependent patient.

Infections associated with Leifsonia aquatica are particularly uncommon. We describe a central venous catheter-associated L. aquatica bacteremia in a hemodialysis-dependent patient. A review of the literature revealed only 1 other case report involving 10 hemodialysis patients with documented L. aquatica bacteremia.