Stenotrophomonas maltophilia natural history and evolution in the airways of adults with cystic fibrosis.

Introduction: Stenotrophomonas maltophilia is an opportunistic pathogen infecting persons with cystic fibrosis (pwCF) and portends a worse prognosis. Studies of S. maltophilia infection dynamics have been limited by cohort size and follow-up. We investigated the natural history, transmission potential, and evolution of S. maltophilia in a large Canadian cohort of 321 pwCF over a 37-year period. Methods: One-hundred sixty-two isolates from 74 pwCF (23%) were typed by pulsed-field gel electrophoresis, and shared pulsotypes underwent whole-genome sequencing. Results: S. maltophilia was recovered at least once in 82 pwCF (25.5%). Sixty-four pwCF were infected by unique pulsotypes, but shared pulsotypes were observed between 10 pwCF. In chronic carriage, longer time periods between positive sputum cultures increased the likelihood that subsequent isolates were unrelated. Isolates from individual pwCF were largely clonal, with differences in gene content being the primary source of genetic diversity objectified by gene content differences. Disproportionate progression of CF lung disease was not observed amongst those infected with multiple strains over time (versus a single) or amongst those with shared clones (versus strains only infecting one patient). We did not observe evidence of patient-to-patient transmission despite relatedness between isolates. Twenty-four genes with ≥ 2 mutations accumulated over time were identified across 42 sequenced isolates from all 11 pwCF with ≥ 2 sequenced isolates, suggesting a potential role for these genes in adaptation of S. maltophilia to the CF lung. Discussion: Genomic analyses suggested common, indirect sources as the origins of S. maltophilia infections in the clinic population. The information derived from a genomics-based understanding of the natural history of S. maltophilia infection within CF provides unique insight into its potential for in-host evolution.

A pragmatic randomized controlled trial of rapid on-site influenza and respiratory syncytial virus PCR testing in paediatric and adult populations.

BACKGROUND: Rapid/point-of-care respiratory virus nucleic acid tests (NAT) may improve oseltamivir, antibiotic, diagnostic test, and hospital bed utilization. Previous randomized controlled trials (RCT) on this topic have not used standard procedures of an accredited healthcare and laboratory system. METHODS: We conducted a parallel RCT at two hospitals [paediatric = Alberta Children's Hospital (ACH); primarily adult = Peter Lougheed Centre (PLC)]. Patients with a respiratory viral testing order were randomized to testing at either a central accredited laboratory (standard arm) or with a rapid polymerase chain reaction test at an on-site accredited laboratory followed by standard testing [rapid on-site test (ROST) arm] based on day of specimen receipt at the laboratory. Patients and clinicians were blinded to assignment. The primary outcome for ACH was inpatient length of stay (LOS) and for PLC was the proportion of inpatients prescribed oseltamivir. RESULTS: 706 patient encounters were included at ACH; 322 assigned to ROST (181 inpatients) and 384 to the standard arm (194 inpatients). 422 patient encounters were included at PLC; 200 assigned to ROST (157 inpatients) and 222 to the standard arm (175 inpatients). The rate of oseltamivir prescription and number of doses given was reduced in PLC inpatients negative for influenza in the ROST arm compared to standard arm [mean 14.9% (95% CI 9.87-21.9) vs. 27.5% (21.0-35.2), p = 0.0135; mean 2.85 doses (SEM 2.39-3.32) vs. 4.17 doses (3.85-4.49) p = 0.022, respectively]. ROST also significantly reduced oseltamivir use at ACH, reduced chest radiographs (ACH), and laboratory test ordering (PLC), but not antibiotic prescriptions. ROST also reduced the median turnaround time by > 24 h (ACH and PLC). The LOS at ACH was not significantly different between the ROST and standard arms [median 4.05 days (SEM 1.79-18.2) vs 4.89 days (2.07-22.9), p = 0.062, respectively]. No adverse events were reported. CONCLUSIONS: In a RCT representing implementation of ROST in an accredited laboratory system, we found that a ROST improved oseltamivir utilization and is the first RCT to show reduced ancillary testing in both paediatric and adult populations. A larger study is required to assess reduction in paediatric LOS as ACH was underpowered. These findings help justify the implementation of rapid on-site respiratory virus testing for inpatients. Trial registration ISRCTN, number 10110119, Retrospectively Registered, 01/12/2021.

Genomic analysis of group A Streptococcus isolated during a correctional facility outbreak of MRSA in 2004.

BACKGROUND: In 2004-2005, an outbreak of impetigo occurred at a correctional facility during a sentinel outbreak of methicillin- resistant Staphylococcus aureus (MRSA) in Alberta, Canada. Next-generation sequencing (NGS) was used to characterize the group A Streptococcus (GAS) isolates and evaluate whether genomic biomarkers could distinguish between those recovered alone and those co-isolated with S. aureus. METHODS: Superficial wound swabs collected from all adults with impetigo during this outbreak were cultured using standard methods. NGS was used to characterize and compare all of the GAS and S. aureus genomes. RESULTS: Fifty-three adults were culture positive for GAS, with a subset of specimens also positive for MRSA (n = 5) or methicillin-sensitive S. aureus (n = 3). Seventeen additional MRSA isolates from this facility from the same time frame (no GAS co-isolates) were also included. All 78 bacterial genomes were analyzed for the presence of known virulence factors, plasmids, and antimicrobial resistance (AMR) genes. Among the GAS isolates were 12 emm types, the most common being 41.2 (n = 27; 51%). GAS genomes were phylogenetically compared with local and public datasets of invasive and non-invasive isolates. GAS genomes had diverse profiles for virulence factors, plasmids, and AMR genes. Pangenome analysis did not identify horizontally transferred genes in the co-infection versus single infections. CONCLUSIONS: GAS recovered from invasive and non-invasive sources were not genetically distinguishable. Virulence factors, plasmids, and AMR profiles grouped by emm type, and no genetic changes were identified that predict co-infection or horizontal gene transfer between GAS and S. aureus.

HISTORIQUE: En 2004­2005, une éclosion d'impétigo s'est manifestée dans un établissement correctionnel pendant une éclosion sentinelle de Staphylococcus aureus résistante à la méthicilline (SRAM) en Alberta, au Canada. Le séquençage de prochaine génération (SPG) a été utilisé pour caractériser les isolats du streptocoque du groupe (SGA) et évaluer si les biomarqueurs génomiques peuvent distinguer ceux qui se rétablissent seuls de ceux qui ont co-isolé le S. aureus. MÉTHODOLOGIE: Les chercheurs ont mis en culture des écouvillons de plaies cutanées superficielles prélevés chez tous les adultes atteints d'impétigo pendant cette éclosion. Ils ont utilisé le SNG pour caractériser et comparer tous les génomes du SPG et du S. aureus récupérés. RÉSULTATS: Cinquante-trois adultes étaient positifs au SGA, un sous-groupe d'échantillons était également positif au SRAM (n = 5) ou au S. aureus (n = 3) sensible à la méthicilline. Dix-sept autres isolats de SRAM provenant de cet établissement pendant la même période (pas de co-isolats du SGA) ont été inclus. Ils ont analysé l'ensemble des 78 génomes bactériens pour déceler la présence de facteurs de virulence connus, de plasmides et de gènes de résistance antimicrobienne (RAM). Parmi les isolats du SGA se trouvaient 12 types d'emm, les plus courants étant 41,2 (n = 27, 51 %). Les génomes du SGA ont été comparés sur le plan phylogénétique aux données locales et publiques sur les isolats invasifs et non invasifs. Les génomes du SGA présentaient divers profils de facteurs de virulence, de plasmides et de gènes de RAM. L'analyse du pangénome n'a pas permis de repérer les gènes transférés dans les génomes de co-infection ou les adaptations génétiques associées à une co-infection plutôt par rapport aux infections uniques. CONCLUSIONS: Le SGA prélevé de sources invasives ou non invasives n'était pas reconnaissable sur le plan génétique. Les facteurs de virulence, les plasmides et les profils de résistance antimicrobienne regroupés par type d'emm ne présentaient pas de changements génétiques prédicteurs d'une co- infection ou d'un transfert génétique horizontal entre le SGA et le S. aureus.

The natural history and genetic diversity of Haemophilus influenzae infecting the airways of adults with cystic fibrosis.

Haemophilus influenzae is a Gram-negative pathobiont, frequently recovered from the airways of persons with cystic fibrosis (pwCF). Previous studies of H. influenzae infection dynamics and transmission in CF predominantly used molecular methods, lacking resolution. In this retrospective cohort study, representative yearly H. influenzae isolates from all pwCF attending the Calgary Adult CF Clinic with H. influenzae positive sputum cultures between 2002 and 2016 were typed by pulsed-field gel electrophoresis. Isolates with shared pulsotypes common to ≥ 2 pwCF were sequenced by Illumina MiSeq. Phylogenetic and pangenomic analyses were used to assess genetic relatedness within shared pulsotypes, and epidemiological investigations were performed to assess potential for healthcare associated transmission. H. influenzae infection was observed to be common (33% of patients followed) and dynamic in pwCF. Most infected pwCF exhibited serial infections with new pulsotypes (75% of pwCF with ≥ 2 positive cultures), with up to four distinct pulsotypes identified from individual patients. Prolonged infection by a single pulsotype was only rarely observed. Intra-patient genetic diversity was observed at the single-nucleotide polymorphism and gene content levels. Seven shared pulsotypes encompassing 39% of pwCF with H. influenzae infection were identified, but there was no evidence, within our sampling scheme, of direct patient-to-patient infection transmission.

Using a systematic approach to strategic innovation in laboratory medicine to bring about change.

There is a growing mismatch with regard to demand, supply, and affordability in healthcare systems in developed countries. Innovation is required to address this, but roadmaps for innovation in laboratory medicine are largely lacking. Advances in process and instrument digitization are driving a revolution in medical laboratory practice but changes are not strategically focused on improved patient care. Laboratory services therefore largely remain transactional so that customer access and experience are suboptimal, especially for vulnerable populations. Laboratory medicine must be integrated back into clinical care pathways, thereby transforming services to be more responsive to end-user needs. Healthcare trends show that patients, physicians, and allied healthcare professionals will increasingly dictate what and how services are provided. Laboratories will be pressed to restructure to address these healthcare trends. Since the primary goal of ambulatory practice is to prevent expensive hospital admissions for patients with complex chronic diseases, specific services (e.g. ambulatory clinics, surgeries, deliveries, procedures) that could be safely provided in the community are moving out of acute care hospitals. This review addresses the existing barriers to innovation faced by medical/scientific and managerial services as well as outlines a systematic approach used by other industries to bring about transformative change. Enabling disruptive innovation that improves the clinical and economic effectiveness of laboratory practice is critical to sustain clinically relevant services as an essential cornerstone of patient care within the healthcare systems of developed countries.

Age and sex-specific incidence rates of group A streptococcal pharyngitis between 2010 and 2018: a population-based study.

Aim: Group A streptococcus (GAS) pharyngitis is a common clinical infection with significant morbidity but remains understudied. Materials & methods: We sought to assess the rates of testing and incidence of GAS pharyngitis in Calgary, Alberta based on age and sex. Results: A total of 1,074,154 tests were analyzed (58.8% female, mean age 24.8 years) of which 16.6% were positive. Age-standardized testing and positivity was greatest in the 5-14 years age group and lowest in persons over 75 years. Females had greater rates of testing and positivity throughout. Testing rates (incidence rate ratios: 1.40, 95% CI: 1.39-1.41) and case rates (incidence rate ratios: 1.36, 95% CI: 1.33-1.39) increased over time. Conclusion: Future studies should focus on evaluating disparities in testing and treatment outcomes to optimize the approach to this infection.

Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory.

This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.

Epidemiology of E. coli in Cystic Fibrosis Airways Demonstrates the Capacity for Persistent Infection but Not Patient-Patient Transmission.

Escherichia coli is frequently isolated from the respiratory secretions of cystic fibrosis (CF) patients yet is not considered a classical CF pathogen. Accordingly, little is known about the natural history of this organism in the CF airways, as well as the potential for patient-to-patient transmission. Patients attending the Calgary Adult CF Clinic (CACFC) between January 1983 and December 2016 with at least one E. coli-positive sputum culture were identified by retrospective review. Annual E. coli isolates from the CACFC biobank from each patient were typed by pulsed-field gel electrophoresis (PFGE) and isolates belonging to shared pulsotypes were sequenced. Single nucleotide polymorphism (SNP) and phylogenetic analysis were used to investigate the natural history of E. coli infection and identify potential transmission events. Forty-five patients with E. coli-positive sputum cultures were identified. Most patients had a single infection episode with a single pulsotype, while replacement of an initial pulsotype with a second was observed in three patients. Twenty-four had E. coli recovered from their sputum more than once and 18 patients had persistent infections (E. coli carriage >6 months with ≥3 positive cultures). Shared pulsotypes corresponded to known extraintestinal pathogenic E. coli strains: ST-131, ST-73, and ST-1193. Phylogenetic relationships and SNP distances among isolates within shared pulsotypes were consistent with independent acquisition of E. coli by individual patients. Most recent common ancestor date estimates of isolates between patients were inconsistent with patient-to-patient transmission. E. coli infection in CF is a dynamic process that appears to be characterized by independent acquisition within our patient population and carriage of unique sets of strains over time by individual patients.

Is the Utilization of Helicobacter pylori Stool Antigen Tests Appropriate in an Urban Canadian Population?

OBJECTIVES: Helicobacter pylori stool antigen test (HpSAT) appropriateness was investigated by assessing its testing and positivity rates in Calgary, Canada. METHODS: The laboratory information system was accessed for all patients who received an HpSAT in 2018. Testing volume, test results, age, and sex of patients were collected. Sociodemographic risk factors and geospatial analysis were performed by matching laboratory data to the 2016 census data. Testing appropriateness was defined as a concordance between testing and positivity rates for each sociodemographic variable. RESULTS: In 2018, 25,518 H pylori stool antigen tests were performed in Calgary, with an overall positivity rate of 14.7%. Geospatial mapping demonstrated significant distribution variations of testing and positivity rates of HpSAT in the city. Certain sociodemographic groups studied (eg, recent immigrants) appeared to be appropriately tested (testing rate relative risk [RR] = 2.26, positivity rate RR = 4.32; P < .0001), while other groups (eg, male) may have been undertested (testing rate RR = 0.85, positivity rate RR = 1.14; P < .0001). CONCLUSIONS: Determining concordance of testing and positivity rate of a laboratory test can be used for assessing testing appropriateness for other diseases in other jurisdictions. This study demonstrated some at-risk patients may be missed for H pylori testing.

Essential role of laboratory physicians in transformation of laboratory practice and management to a value-based patient-centric model.

The laboratory is a vital part of the continuum of patient care. In fact, there are few programs in the healthcare system that do not rely on ready access and availability of complex diagnostic laboratory services. The existing transactional model of laboratory "medical practice" will not be able to meet the needs of the healthcare system as it rapidly shifts toward value-based care and precision medicine, which demands that practice be based on total system indicators, clinical effectiveness, and patient outcomes. Laboratory "value" will no longer be focused primarily on internal testing quality and efficiencies but rather on the relative cost of diagnostic testing compared to direct improvement in clinical and system outcomes. The medical laboratory as a "business" focused on operational efficiency and cost-controls must transform to become an essential clinical service that is a tightly integrated equal partner in direct patient care. We would argue that this paradigm shift would not be necessary if laboratory services had remained a "patient-centric" medical practice throughout the last few decades. This review is focused on the essential role of laboratory physicians in transforming laboratory practice and management to a value-based patient-centric model. Value-based practice is necessary not only to meet the challenges of the new precision medicine world order but also to bring about sustainable healthcare service delivery.

Sociodemographic and geospatial associations with community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections in a large Canadian city: an 11 year retrospective study.

BACKGROUND: The first Canadian outbreak of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) was identified in 2004 in Calgary, Alberta. Using a novel model of MRSA population-based surveillance, sociodemographic risk associations, yearly geospatial dissemination and prevalence of CA-MRSA infections over an 11 year period was identified in an urban healthcare jurisdiction of Calgary. METHODS: Positive MRSA case records, patient demographics and laboratory data were obtained from a centralized Laboratory Information System of Calgary Laboratory Services in Calgary, Alberta, Canada between 2004 and 2014. Public census data was obtained from Statistics Canada, which was used to match with laboratory data and mapped using Geographic Information Systems. RESULTS: During the study period, 52.5% of positive MRSA infections in Calgary were CA-MRSA cases. The majority were CMRSA10 (USA300) clones (94.1%; n = 4255), while the remaining case (n = 266) were CMRSA7 (USA400) clones. Period prevalence of CMRSA10 increased from 3.6 cases/100000 population in 2004, to 41.3 cases/100000 population in 2014. Geospatial analysis demonstrated wide dissemination of CMRSA10 annually in the city. Those who are English speaking (RR = 0.05, p <  0.0001), identify as visible minority Chinese (RR = 0.09, p = 0.0023) or visible minority South Asian (RR = 0.25, p = 0.015), and have a high median household income (RR = 0.27, p <  0.0001) have a significantly decreased relative risk of CMRSA10 infections. CONCLUSIONS: CMRSA10 prevalence increased between 2004 and 2007, followed by a stabilization of cases by 2014. Certain sociodemographic factors were protective from CMRSA10 infections. The model of MRSA population-surveillance and geomap outbreak events can be used to track the epidemiology of MRSA in any jurisdiction.

Benefits and risks of standardization, harmonization and conformity to opinion in clinical laboratories.

Large laboratory systems that include facilities with a range of capabilities and capacity are being created within consolidated healthcare systems. This paradigm shift is being driven by administrators and payers seeking to achieve resource efficiencies and to conform practice to the requirements of computerization as well as the adoption of electronic medical records. Although standardization and harmonization of practice improves patient care outcomes and operational efficiencies, administratively driven practice conformity (conformity to opinion) also has serious drawbacks and may lead to significant system failure. Juxtaposition of the distinct philosophical approaches of physicians and scientists (i.e. "professionalism") versus administrators and managers (i.e. "managerialism") towards bringing about conformity of the laboratory system inherently creates conflict. Despite an administrative edict to "perform all tests using the same methods" regardless of available "best practice" evidence to do so, medical/scientific input on these decisions is critical to ensure quality and safety of patient care. Innovation within the laboratory system, including the adoption of advanced technologies, practices, and personalized medicine initiatives, will be enabled by balancing the relentless drive by non-medical administration to meet "business" requirements, the medical responsibility to provide the best care possible, and customizing practice to meet individual patient care needs.

Automation and artificial intelligence in the clinical laboratory.

The daily operation of clinical laboratories will be drastically impacted by two disruptive technologies: automation and artificial intelligence (the development and use of computer systems able to perform tasks that normally require human intelligence). These technologies will also expand the scope of laboratory medicine. Automation will result in increased efficiency but will require changes to laboratory infrastructure and a shift in workforce training requirements. The application of artificial intelligence to large clinical datasets generated through increased automation will lead to the development of new diagnostic and prognostic models. Together, automation and artificial intelligence will support the move to personalized medicine. Changes in pathology and clinical doctoral scientist training will be necessary to fully participate in these changes. KEYWORDS: Automation; artificial intelligence; deep learning; laboratory medicine.

Multidrug-resistant Aeromonas hydrophila causing fatal bilateral necrotizing fasciitis in an immunocompromised patient: a case report.

BACKGROUND: Aeromonas hydrophila is a water-dwelling, gram-negative rod-shaped bacterium, associated with diarrheal illness and, less commonly, necrotizing skin and soft tissue infections, especially among immunocompromised patients. Necrotizing fasciitis is associated with a high mortality rate, especially when caused by Aeromonas spp. Our patient was infected with an extremely aggressive form of multidrug-resistant Aeromonas spp. that produced both an extended-spectrum ß-lactamase and an AmpC enzyme. Aeromonads are being recognized as important emerging pathogens because of their inherent antibiotic resistance profiles compounded by other virulence factors. These difficult-to-treat organisms can have significant implications in both clinical and public health settings. CASE PRESENTATION: A 37-year-old Caucasian male with immunosuppression due to aplastic anemia being treated with cyclosporine, presented to hospital with relapsed disease. While in hospital, he subsequently developed overwhelming sepsis secondary to bilateral lower extremity necrotizing fasciitis. The necrotizing fasciitis was caused by a multidrug-resistant strain of A. hydrophila. Despite broad-spectrum antibiotics and aggressive surgical debridement, he succumbed to this severe invasive infection. CONCLUSIONS: Necrotizing fasciitis caused by Aeromonas spp. is a rare infection that may have a poor clinical outcome, particularly if the diagnosis is delayed and/or the organism is highly virulent and multidrug resistant. Enhanced education of clinicians and microbiologists is required to prevent unnecessary complications and improve survival.

Combating the HIV reservoirs.

Impressive advances have been made in the treatment and management of HIV-1 infected individuals. Combination antiretroviral therapy (cART) has turned HIV-1 infection from an almost invariable deadly infectious disease, to a lifelong manageable infectious disease. However, a cure or vaccine has not been forthcoming. A major problem in HIV-1 infection is the persistent and latently infected cellular and tissue reservoirs. One of these reservoirs is the Gut Associated Lymphoid tissue (GALT), which has been the research focus of our group. Our group and others have shown that HIV-1 evolves differently in different parts of the gastro intestinal tract, which also appears to affect the development of antiretroviral drug resistance. The GALT is not the only reservoir. HIV-1 continues to persist and evolve in various other cell and tissue reservoirs despite intense and apparent successful antiretroviral therapy. Moreover, drug resistance mutations remain prevalent under therapy and successful viral suppression. In addition to finding a vaccine, the research on combating and eradicating the HIV-1 viral reservoirs has also been an important focus of HIV-1 cure strategies. We will discuss some of the research findings on reservoirs in the context of some of the HIV-1 cure approaches.

Evaluation of Simplexa Group A Strep Direct Kit Compared to Hologic Group A Streptococcal Direct Assay for Detection of Group A Streptococcus in Throat Swabs.

Diagnosis of bacterial pharyngitis is confirmed by detection of group A Streptococcus (GAS) in patient throat samples. Testing of throat samples has historically relied on culture, but new molecular methods allow much faster test turnaround time (i.e., same day versus 48 to 72 h for culture). Our laboratory uses the Hologic GAS Direct (GASD) assay for screening more than 125,000 throat samples per year. Simplexa GAS Direct is a new real-time quantitative PCR (qPCR) assay that does not require initial DNA extraction. Performance of Simplexa qPCR was compared to GASD. A total of 289 throat swabs were collected from patients attending ambulatory clinics in Calgary, Alberta, Canada. A total of 60 (20.8%) of the samples were initially GAS positive by either method: 54 by both methods, 4 by Simplex qPCR alone, and 2 by GASD alone. An in-house PCR using a unique GAS primer set was used to resolve the 6 discrepant results. Overall, GASD compared to Simplexa qPCR had a sensitivity, specificity, positive predictive value, and negative predictive value of 93.1% versus 100%, 100% versus 100%, 100% versus 100%, and 98.31% versus 100%, respectively. Implementation of Simplexa qPCR in our laboratory setting would cost more but allow the high sample volume to be reported in half the time and save 0.62 medical laboratory technician (MLT) full-time equivalent (FTE). In comparison to culture, the implementation of Simplexa qPCR would save 2.79 medical laboratory assistant (MLA) FTE plus 0.94 MLT FTE. Simplexa qPCR has improved performance and diagnostic efficiency in a high-volume laboratory compared to GASD for GAS detection in throat swabs.

Sociodemographic correlates of urine culture test utilization in Calgary, Alberta.

BACKGROUND: Many clinical practice guidelines encourage diagnosis and empiric treatment of lower urinary tract infection without laboratory investigation; however, urine culture testing remains one of the largest volume tests in the clinical microbiology laboratory. In this study, we sought to determine if there were specific patient groups to which increased testing was directed. To do so, we combined laboratory data on testing rates with Census Canada sociodemographic data. METHODS: Urine culture testing data was obtained from the Calgary Laboratory Services information system for 2011. We examined all census dissemination areas within the city of Calgary and, for each area, testing rates were determined for age and gender cohorts. We then compared these testing rates to sociodemographic factors obtained from Census Canada and used Poisson regression and generalized estimating equations to test associations between testing rates and sociodemographic variables. RESULTS: Per capita urine culture testing is increasing in Calgary. For 2011, 100,901 individuals (9.2% of all people) received urine cultures and were included in this analysis. The majority of cultures were received from the community (67.9%). Substantial differences in rate of testing were observed across the city. Most notably, urine culture testing was drastically lower in areas of high (≥ $100000) household income (RR = 0.07, p < 0.0001) and higher employment rate (RR = 0.36, p < 0.0001). Aboriginal - First Nations status (RR = 0.29, p = 0.0008) and Chinese visible minority (RR = 0.67, p = 0.0005) were also associated with decreased testing. Recent immigration and visible minority status of South Asian, Filipino or Black were not significant predictors of urine culture testing. Females were more likely to be tested than males (RR = 2.58, p < 0.0001) and individuals aged 15-39 were the most likely to be tested (RR = 1.69, p < 0.0001). CONCLUSIONS: Considerable differences exist in urine culture testing across Calgary and these are associated with a number of sociodemographic factors. In particular, areas of lower socioeconomic standing had significantly increased rates of testing. These observations highlight specific groups that should be targeted to improve healthcare delivery and, in turn, enhance laboratory utilization.

Eggerthella lenta Bloodstream Infections Are Associated With Increased Mortality Following Empiric Piperacillin-Tazobactam (TZP) Monotherapy: A Population-based Cohort Study.

Background: Eggerthella lenta is a anaerobic gram-positive bacilli associated with polymicrobial intraabdominal infections. Recently, E. lenta was recognized as an important cause of anaerobic bloodstream infections (BSIs) associated with high mortality. Eggerthella lenta has been reported to have high minimal inhibitory concentrations (MICs) to piperacillin-tazobactam (TZP), a broad-spectrum antibiotic with anaerobic coverage commonly used in multiple centers for empiric treatment of abdominal sepsis. Methods: We describe a retrospective population-based analysis of invasive E. lenta infections from 2009 through 2015. A logistic regression analysis for 30-day mortality risk factors was conducted. Results: We identified 107 E. lenta infections, 95 (89%) were BSIs, 11 (10%) skin and soft tissue infections, and 1 intraabdominal abscess. Polymicrobial infections were found in 40%; 72% of isolates were from a gastrointestinal source, most commonly appendicitis (33%) of which two-thirds were perforated. TZP MIC50 and MIC90 for E. lenta isolates were 32 µg/mL and 64 µg/mL, respectively. The overall 30-day mortality for BSI was 23% and was independently associated with empiric TZP monotherapy (odds ratio [OR], 4.4; 95% confidence interval [CI], 1.2-16; P = .02) and intensive care unit stay (OR, 6.2; 95% CI, 1.4-27.3; P = .01). Thirty-day mortality rates were significantly influenced by the use of different TZP MIC breakpoints. Conclusions: Our results demonstrate the increased recognition of E. lenta as an anaerobic opportunistic pathogen and highlight the need for improved empiric antimicrobial guidelines and TZP MIC breakpoints with better correlation to clinical outcomes to guide appropriate management of invasive E. lenta infections.

Examining sociodemographic risk factors for Chlamydia trachomatis infection: a population-based cohort study.

AIM: Chlamydia trachomatis is the most prevalent bacterial sexually transmitted infection in developed nations and is an important public health concern. We aimed to assess the factors associated with testing and positivity of C. trachomatis in a large population. METHODS: A retrospective study of a large Canadian health region was undertaken using 2011 census and laboratory data. Demographic and socioeconomic data from the national household survey were linked to microbiologic data for C. trachomatis. Multivariable generalized estimating equation models were constructed to examine relative risk for C. trachomatis testing and positivity. RESULTS: For testing and positivity, female sex and younger age groups were associated with increased risk. University education and South Asian ethnicity were associated with lower risk of positivity. CONCLUSION: Incorporating socio-demographic factors will be critical to the success of future sexually transmitted infection public health programs.

Detection of Plasmodium Infection by the illumigene Malaria Assay Compared to Reference Microscopy and Real-Time PCR.

Malaria is one of the leading causes of infectious disease in travelers returning from the tropics. The diagnosis of malaria is typically performed by examining Giemsa-stained thick and thin peripheral blood smears, which is time consuming, labor intensive, and requires high levels of proficiency. Alternatively, loop-mediated isothermal amplification (LAMP) is a new molecular method, which is rapid, sensitive, and requires less capital equipment and technological training. We conducted a retrospective study comparing two formats of a commercial LAMP assay (Meridian illumigene malaria [M] and malaria Plus [MP]) versus reference microscopy on archived blood specimens (n = 140) obtained from unique returning travelers suspected of having malaria. Discrepant results were resolved by either repeat testing or a laboratory developed ultrasensitive real-time PCR method. On initial testing, the Meridian illumigene M and MP kits had sensitivities of 97.3% (95% confidence interval [CI], 90.7 to 99.7%) and 100.0% (95.1 to 100.0%) and specificities of 93.8% (84.8 to 98.3%) and 91.5% (81.3 to 97.2%), respectively, versus reference microscopy. We project a significant cost reduction in low prevalence settings where malaria is not endemic with LAMP-based malaria screening given the excellent negative predictive value achieved with LAMP.