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1.
Article in English | MEDLINE | ID: mdl-38698945

ABSTRACT

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.

2.
J Clin Microbiol ; 62(5): e0144523, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38557148

ABSTRACT

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.


Subject(s)
Automation, Laboratory , Bacteriological Techniques , Methicillin-Resistant Staphylococcus aureus , Sensitivity and Specificity , Staphylococcal Infections , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Humans , Staphylococcal Infections/diagnosis , Staphylococcal Infections/microbiology , Automation, Laboratory/methods , Bacteriological Techniques/methods , Automation/methods , Colorimetry/methods , Artificial Intelligence
3.
BMC Public Health ; 22(1): 736, 2022 04 13.
Article in English | MEDLINE | ID: mdl-35418084

ABSTRACT

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.


Subject(s)
Borrelia burgdorferi , Ixodes , Lyme Disease , Tick Bites , Animals , Humans , Lyme Disease/epidemiology , Models, Statistical , Ontario/epidemiology
4.
Sci Rep ; 12(1): 1337, 2022 01 25.
Article in English | MEDLINE | ID: mdl-35079040

ABSTRACT

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.


Subject(s)
Bacteriological Techniques/methods , Culture Media , DNA, Bacterial/analysis , Staphylococcus/isolation & purification , Humans , Retrospective Studies
5.
Diagn Microbiol Infect Dis ; 102(3): 115609, 2022 Mar.
Article in English | MEDLINE | ID: mdl-34933188

ABSTRACT

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.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19 Testing , Humans , Ontario , Prospective Studies , Sensitivity and Specificity , Tertiary Care Centers
6.
Diagn Microbiol Infect Dis ; 101(4): 115514, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34418823

ABSTRACT

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.


Subject(s)
Asymptomatic Infections , COVID-19 Serological Testing/methods , COVID-19 Testing/methods , COVID-19/virology , SARS-CoV-2/isolation & purification , COVID-19/diagnosis , Canada , Humans , Immunologic Tests , Nasopharynx/virology , Predictive Value of Tests , Prospective Studies , Sensitivity and Specificity
7.
mSphere ; 6(3)2021 05 05.
Article in English | MEDLINE | ID: mdl-33952657

ABSTRACT

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.


Subject(s)
Genetic Variation/genetics , Genome, Viral/genetics , Mutation Rate , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Base Sequence , COVID-19/pathology , Humans , Ontario , Phylogeny , Sequence Analysis, RNA
8.
J Gen Intern Med ; 36(1): 162-169, 2021 01.
Article in English | MEDLINE | ID: mdl-33107007

ABSTRACT

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.


Subject(s)
COVID-19 Testing/statistics & numerical data , COVID-19/diagnosis , Risk Assessment/standards , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , COVID-19/transmission , Community-Acquired Infections/diagnosis , Community-Acquired Infections/epidemiology , Community-Acquired Infections/transmission , Female , Humans , Logistic Models , Male , Middle Aged , Ontario/epidemiology , Pandemics , Reverse Transcriptase Polymerase Chain Reaction , Risk Assessment/methods , SARS-CoV-2 , Surveys and Questionnaires , Young Adult
9.
Access Microbiol ; 2(1): acmi000078, 2020.
Article in English | MEDLINE | ID: mdl-33062937

ABSTRACT

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.

10.
J Fungi (Basel) ; 5(4)2019 Nov 10.
Article in English | MEDLINE | ID: mdl-31717662

ABSTRACT

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.

11.
Diagn Microbiol Infect Dis ; 95(3): 114866, 2019 Nov.
Article in English | MEDLINE | ID: mdl-31473033

ABSTRACT

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.


Subject(s)
Bacteriological Techniques/methods , Molecular Diagnostic Techniques/methods , Pharynx/microbiology , Streptococcal Infections/diagnosis , Streptococcus pyogenes/isolation & purification , Adult , Child , Humans , Nucleic Acid Amplification Techniques , Sensitivity and Specificity , Streptococcal Infections/microbiology
12.
J Clin Virol ; 113: 35-38, 2019 04.
Article in English | MEDLINE | ID: mdl-30856386

ABSTRACT

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.


Subject(s)
Herpesvirus 1, Human/isolation & purification , Herpesvirus 2, Human/isolation & purification , Molecular Diagnostic Techniques/instrumentation , Molecular Diagnostic Techniques/standards , Adolescent , Adult , Child , Child, Preschool , Female , Humans , Male , Nucleic Acid Amplification Techniques/instrumentation , Nucleic Acid Amplification Techniques/standards , Reagent Kits, Diagnostic/standards , Sensitivity and Specificity , Time Factors , Virology/methods , Virology/standards
13.
J Am Vet Med Assoc ; 253(7): 897-906, 2018 Oct 01.
Article in English | MEDLINE | ID: mdl-30211643

ABSTRACT

OBJECTIVE To describe use of a modified open castration technique with a scrotal approach and primary closure in equids. DESIGN Prospective case series. ANIMALS 38 client-owned, sexually intact male equids. PROCEDURES With owner consent, elective castration was performed with a modified open technique on patients (1 pony, 1 miniature horse, and 36 horses of other breeds) under general anesthesia. The procedure included minimal dissection into the scrotal region for removal of testes, with cremaster muscles left intact and the parietal vaginal tunic closed in place. Primary closure of surgical wounds was performed. Patients were monitored for signs of complications. Signalment, surgery-related variables, results of ultrasonographic imaging, postoperative treatments, and outcomes were recorded. Follow-up information was obtained from owners ≥ 6 months after surgery. Medical records were reviewed, and descriptive data were reported. RESULTS Median anesthesia and surgery times were 113.5 and 60 minutes, respectively. Duration of hospitalization ranged from 1 to 3 days. No intraoperative complications were observed. Postoperative complications (moderate swelling in the scrotal region) developed in 2 of 38 (5%) patients. Mild scrotal swelling (n = 5) and transient pyrexia (typically mild; 9) also occurred; no patients had signs of postoperative bleeding, infection, or colic. All equids gradually returned to exercise beginning 10 days after the procedure. Cosmetic results were considered excellent. CONCLUSIONS AND CLINICAL RELEVANCE The modified castration technique was considered simple to perform and advantageous because of the low complication rate, excellent cosmetic results, and prompt return to intended use after surgery.


Subject(s)
Horses/surgery , Minimally Invasive Surgical Procedures/veterinary , Orchiectomy/veterinary , Animals , Length of Stay , Male , Minimally Invasive Surgical Procedures/methods , Orchiectomy/methods , Postoperative Complications/veterinary , Prospective Studies , Suture Techniques/veterinary , Treatment Outcome
14.
BMC Res Notes ; 11(1): 514, 2018 Jul 28.
Article in English | MEDLINE | ID: mdl-30055653

ABSTRACT

OBJECTIVE: Molecular methods to detect diarrheal pathogens are increasingly being used in place of conventional methods. We compared a new multiplex real-time PCR assay for detection of both bacterial and viral gastroenteritis agents, the Allplex™ Gastrointestinal Panel Assays (AGPA), to conventional methods (stool culture for bacterial pathogens and electron microscopy (EM) for viral pathogens). RESULTS: Gastrointestinal viruses, in particular norovirus genogroup II viruses, were detected by the AGPA in a high number of specimens that were negative by EM. For bacterial pathogens, the AGPA was able to detect the organisms grown in culture with high sensitivity and additionally detected several types of E. coli, such as enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC), and non-O157 Shiga toxin-producing E. coli (STEC), that could not be detected with conventional culture methods. Overall, the AGPA had a > 2-fold higher detection rate than the conventional methods, with 24/135 (17.8%) samples positive by conventional methods and 60/135 (44.4%) by AGPA. Thus, diarrhea pathogen detection rates increased substantially with the use of the AGPA as compared to conventional methods.


Subject(s)
Escherichia coli/isolation & purification , Gastroenteritis/microbiology , Multiplex Polymerase Chain Reaction , Bacteriological Techniques/methods , Escherichia coli/genetics , Escherichia coli Infections/diagnosis , Feces , Humans , Sensitivity and Specificity
15.
Vet Surg ; 47(4): 555-565, 2018 May.
Article in English | MEDLINE | ID: mdl-29603790

ABSTRACT

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.


Subject(s)
Arthroscopy/veterinary , Horse Diseases/surgery , Osteochondritis Dissecans/veterinary , Tarsal Joints/surgery , Animals , Arthroscopy/methods , Female , Horses , Male , Osteochondritis Dissecans/surgery , Retrospective Studies
16.
J Microbiol Methods ; 136: 17-20, 2017 05.
Article in English | MEDLINE | ID: mdl-28267570

ABSTRACT

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and chromogenic media are widely used in clinical microbiology laboratories to facilitate the rapid selection and identification of pathogens. The aim of this study was to evaluate whether usage of chromogenic media limits the diagnostic performance of MALDI-TOF MS for microbial identification. A total of 386 microorganisms collected and analyzed at five laboratories were included. Isolates were cultured on relevant chromogenic media and non-selective agar plates in parallel and identified using the Bruker MALDI-TOF MS. Among the tested isolates, no misidentification was recorded and there was no medium-related difference in the identification level. However, score values were overall slightly but significantly lower for isolates grown on chromogenic media. In conclusion, the use of chromogenic culture media tested here had no relevant impact on MALDI-TOF MS performance for diagnostic purposes.


Subject(s)
Bacteria/growth & development , Bacteria/isolation & purification , Bacteriological Techniques/methods , Chromogenic Compounds/chemistry , Culture Media/chemistry , Fungi/growth & development , Fungi/isolation & purification , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Bacteria/pathogenicity , Bacterial Infections/diagnosis , Fungi/pathogenicity , Laboratories , Limit of Detection , Methicillin-Resistant Staphylococcus aureus/growth & development , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Methicillin-Resistant Staphylococcus aureus/pathogenicity , Mycoses/diagnosis , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation , Vancomycin-Resistant Enterococci/growth & development , Vancomycin-Resistant Enterococci/isolation & purification , Vancomycin-Resistant Enterococci/pathogenicity
17.
Am J Infect Control ; 44(4): 425-31, 2016 Apr 01.
Article in English | MEDLINE | ID: mdl-26804301

ABSTRACT

BACKGROUND: Pneumocystis pneumonia is a severe opportunistic fungal infection. Outbreaks among renal transplant recipients have been reported in Europe and Japan, but never in North America. METHODS: We conducted a retrospective case-control study among adult renal transplant recipients at a Canadian center, using a 3:1 matching scheme. Ten cases and 30 controls were matched based on initial transplantation date, and all patients received prophylaxis with trimethoprim-sulfamethoxazole for 1 year posttransplantation. RESULTS: The median time between transplantation and infection was 10.2 years, and all patients survived. Compared with controls, case patients had statistically lower estimated glomerular filtration rate (29.3 mL/min vs 66.3 mL/min; P = .028) and lymphopenia (0.51 × 10(9)/L vs 1.25 × 10(9)/L; P = .002). Transmission mapping revealed significant overlap in the clinic and laboratory visits among case vs control patients (P = .0002). One hundred percent of patients (4 out of 4) successfully genotyped had the same strain of Pneumocystis jirovecii. CONCLUSIONS: Our study demonstrated an outbreak of pneumocystis more than 10 years following initial transplantation, despite using recommended initial prophylaxis. We identified low estimated glomerular filtration rate and lymphopenia as risk factors for infection. Overlapping ambulatory care visits were identified as important potential sources of infection transmission, suggesting that institutions should re-evaluate policy and infrastructure strategies to interrupt transmission of respiratory pathogens.


Subject(s)
Disease Outbreaks , Disease Transmission, Infectious , Kidney Transplantation , Pneumocystis carinii/isolation & purification , Pneumonia, Pneumocystis/epidemiology , Pneumonia, Pneumocystis/transmission , Transplant Recipients , Adult , Aged , Aged, 80 and over , Ambulatory Care/methods , Canada/epidemiology , Case-Control Studies , Female , Genotype , Humans , Infection Control/methods , Male , Middle Aged , Pneumocystis carinii/classification , Pneumocystis carinii/genetics , Retrospective Studies , Risk Factors , Young Adult
19.
J Clin Microbiol ; 53(7): 2225-9, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25948610

ABSTRACT

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.


Subject(s)
Bacterial Proteins/genetics , Carbon-Oxygen Ligases/genetics , Enterococcus/genetics , Enterococcus/isolation & purification , Gene Order , Genes, Bacterial , Anti-Bacterial Agents/pharmacology , Chromosomes, Bacterial , Drug Resistance, Bacterial , Enterococcus/drug effects , Gram-Positive Bacterial Infections , Humans , Male , Middle Aged , Plasmids , Teicoplanin/pharmacology , Vancomycin/pharmacology
20.
PLoS One ; 9(11): e111986, 2014.
Article in English | MEDLINE | ID: mdl-25386908

ABSTRACT

BACKGROUND: The tuberculin skin test (TST) is the standard test used to screen for latent TB infection (LTBI) in the northern Canadian territory of Nunavut. Interferon gamma release assays (IGRA) are T cell blood-based assays to diagnose LTBI. The Bacillus Calmette-Guerin (BCG) vaccine is part of the routine immunization schedule in Nunavut. The objective of this study was to test the feasibility, and predictors of discordance between the Tuberculin Skin Test (TST) and the IGRA assay in a medically under-serviced remote arctic Aboriginal population. METHODS: Both the TST and QuantiFERON-TB Gold (Qiagen group) IGRA tests were offered to people in their homes as part of a public health campaign aimed at high TB risk residential areas in Iqaluit, Nunavut, Canada. Feasibility was measured by the capacity of the staff to do the test successfully as measured by the proportion of results obtained. RESULTS: In this population of predominantly young Inuit who were mostly BCG vaccinated, the use of IGRA for the diagnosis of LTBI was feasible. IGRA testing resulted in more available test results reaching patients (95.6% vs 90.9% p = 0.02) but took longer (median 8 days (IGRA) vs 2 days (TST), p value < 0.0001). 44/256 participants (17.2%) had discordant results. Multivariable regression analysis suggested that discordant results were most likely to have received multiple BCG vaccinations (RR 20.03, 95% CI, 3.94-101.82)), followed by BCG given post infancy (RR 8.13, 95% CI, 2.54-26.03)) and then to a lesser degree when BCG was given in infancy (RR 6.43, 95% CI, 1.72-24.85). INTERPRETATION: IGRA is feasible in Iqaluit, Nunavut, a remote Arctic community. IGRA testing results in more test results available to patients compared to TST. This test could result in fewer patients requiring latent TB treatment among those previously vaccinated with BCG in a region with limited public health human resources.


Subject(s)
Interferon-gamma Release Tests/methods , Latent Tuberculosis/diagnosis , Tuberculin Test/methods , Adult , Feasibility Studies , Female , Humans , Inuit , Male , Nunavut , Young Adult
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