Rapid Increase in SARS-CoV-2 P.1 Lineage Leading to Codominance with B.1.1.7 Lineage, British Columbia, Canada, January-April 2021.

Several severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) emerged in late 2020; lineage B.1.1.7 initially dominated globally. However, lineages B.1.351 and P.1 represent potentially greater risk for transmission and immune escape. In British Columbia, Canada, B.1.1.7 and B.1.351 were first identified in December 2020 and P.1 in February 2021. We combined quantitative PCR and whole-genome sequencing to assess relative contribution of VOCs in nearly 67,000 infections during the first 16 weeks of 2021 in British Columbia. B.1.1.7 accounted for <10% of screened or sequenced specimens early on, increasing to >50% by week 8. P.1 accounted for <10% until week 10, increased rapidly to peak at week 12, and by week 13 codominated within 10% of rates of B.1.1.7. B.1.351 was a minority throughout. This rapid expansion of P.1 but suppression of B.1.351 expands our understanding of population-level VOC patterns and might provide clues to fitness determinants for emerging VOCs.

Development and validation of a Pneumocystis jirovecii real-time polymerase chain reaction assay for diagnosis of Pneumocystis pneumonia.

BACKGROUND: Pneumocystis jirovecii (PJ), a pathogenic fungus, causes severe interstitial Pneumocystis pneumonia (PCP) among immunocompromised patients. A laboratory-developed real-time polyermase chain reaction (PCR) assay was validated for PJ detection to improve diagnosis of PCP. METHODS: Forty stored bronchoalveolar lavage (BAL) samples (20 known PJ positive [PJ+] and 20 known PJ negative [PJ-]) were initially tested using the molecular assay. Ninety-two sequentially collected BAL samples were then analyzed using an immunofluorescence assay (IFA) and secondarily tested using the PJ real-time PCR assay. Discrepant results were resolved by retesting BAL samples using another real-time PCR assay with a different target. PJ real-time PCR assay performance was compared with the existing gold standard (ie, IFA) and a modified gold standard, in which a true positive was defined as a sample that tested positive in two of three methods in a patient suspected to have PCP. RESULTS: Ninety of 132 (68%) BAL fluid samples were collected from immunocompromised patients. Thirteen of 92 (14%) BALs collected were PJ+ when tested using IFA. A total of 40 BAL samples were PJ+ in the present study including: all IFA positive samples (n=13); all referred PJ+ BAL samples (n=20); and seven additional BAL samples that were IFA negative, but positive using the modified gold standard. Compared with IFA, the PJ real-time PCR had sensitivity, specificity, and positive and negative predictive values of 100%, 91%, 65% and 100%, respectively. Compared with the modified gold standard, PJ real-time PCR had a sensitivity, specificity, and positive and negative predictive values of 100%. CONCLUSION: PJ real-time PCR improved detection of PJ in immunocompromised patients.

HISTORIQUE: Le Pneumocystis jirovecii (PJ), un champignon pathogène, provoque une grave pneumonie à Pneumocystis interstitielle (PPC) chez les patients immunodéprimés. Les chercheurs ont validé un test de réaction en chaîne par polymérase (PCR) en temps réel pour détecter le PJ et ainsi améliorer le diagnostic de PPC. MÉTHODOLOGIE: Les chercheurs ont d'abord vérifié 40 prélèvements de liquide bronchoalvéolaire (LBA) entreposés (20 cas positifs connus au PJ [PJ+] et 20 cas négatifs connus au PJ [PJ−]) au moyen du test moléculaire. Ils ont ensuite analysé 92 prélèvements séquentiels de LBA au moyen d'un test par immunofluorescence (IFA), puis d'un test de PCR en temps réel du PJ. Ils ont résolu les résultats divergents au moyen d'un nouveau test par PCR en temps réel des prélèvements de LBA axée sur une autre cible. Ils ont comparé le résultat du test de PCR en temps réel du PJ à la référence absolue (l'IFA) et à une référence modifiée, dans laquelle un véritable cas positif désignait un prélèvement positif par deux méthodes sur trois chez un patient atteint d'une PPC présumée. RÉSULTATS: Quatre-vingt-dix prélèvements de LBA (68 %) sur 132 provenaient de patients immunodéprimés. Treize prélèvements de LBA (14 %) sur 92 étaient PJ+ d'après l'IFA. Dans la présente étude, 40 prélèvements de LBA étaient PJ+, y compris tous les prélèvements positifs à l'IFA (n=13), tous les prélèvements de LBA PJ+ aiguillés (n=20) et sept autres prélèvements de LBA négatifs à l'IFA, mais positifs selon la référence modifiée. Par rapport à l'IFA, la PCR en temps réel du PJ avait une sensibilité, une spécificité et des valeurs prédictives positive et négative de 100 %, 91 %, 65 % et 100 %, respectivement. Par rapport à la référence modifiée, la PCR en temps réel du PJ avait une sensibilité, une spécificité et des valeurs prédictives positive et négative de 100 %. CONCLUSION: La PCR en temps réel du PJ en améliore la détection chez les patients immunodéprimés.

Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel for detection of pathogens in nasopharyngeal and lower respiratory tract specimens.

This study evaluates the performance of the QIAstat-Dx Respiratory SARS-CoV-2 Panel (RS2P) for the detection of respiratory pathogens. RS2P testing was performed on 440 specimens, including 82 negatives and 358 specimens positive for 1 or more targets (520 targets initially detected). Initial testing was performed on multiple platforms during routine laboratory workflow. Specimens with discordant results on RS2P were re-tested on a different platform to obtain a consensus result based on agreement of 2/3 assays. Percent positive, negative and overall agreement (PPA, PNA, POA), as well as concordance by number of targets and CT value range were calculated. RS2P produced valid results in 439 specimens, with a POA of 91.5 % based on consensus results, with 16/31 (51.6 %) discordant specimens with >1 positive target. When individual targets were examined, PPA, PNA and POA were 93.7 %, 99.9 % and 99.6 % compared to consensus results. Overall, RS2P performed well in detection of respiratory pathogens.

The role of leech water sampling in choice of prophylactic antibiotics in medical leech therapy.

Medical leech therapy (MLT) with Hirudo medicinalis is well established as a treatment for venous congestion of tissue flaps, grafts, and replants. Unfortunately, this treatment is associated with surgical site infections with bacterial species, most commonly Aeromonas hydrophila, which is an obligate symbiot of H. medicinalis. For this reason, prophylactic antibiotics are recommended in the setting of MLT. After culturing Aeromonashydrophila resistant to ciprofloxacin from a tissue specimen from a patient with a failed replant of three digits post-MLT, we performed environmental surveillance cultures and antibiotic susceptibility testing on water collected from leech tanks. This surveillance was performed twice weekly for 2.5 months. Fourteen surveillance cultures demonstrated 21 isolates of Aeromonas species, 71.4% of which were ciprofloxacin susceptible. All isolates were sulfamethoxazole-trimethoprim (SXT) susceptible. The prophylactic antibiotic regimen of choice for leech therapy at our institution is SXT, with culture of tank water to refine antimicrobial choice if necessary. This study demonstrates the importance of regular surveillance to detect resistant Aeromonas species in medical leeches; however optimal practice has not been established.

Evaluation of the Aptima BV and CV/TV assays compared to conventional laboratory based testing methods for the diagnosis of vaginitis.

PURPOSE: Vaginitis is caused by bacterial vaginosis (BV), Candida vaginitis (CV) and Trichomonas vaginalis (TV). This retrospective study evaluates the performance of the Aptima CV/TV, and BV assays on the automated Panther system. METHODS: Two hundred forty-two multitest swabs were tested on the CV/TV assay and 422 on the BV assay. Positive and negative percent agreement (PPA, NPA) of the Candida glabrata (CG), Candida species group (CSG), TV and BV targets were calculated using a modified gold standard, with review of Gram smear and the usage of the Allplex Vaginitis Screening Assay to resolve discrepancies. RESULTS: The PPA and NPA were respectively 98.4% and 95.9% for BV, 100% and 95.4% for CSG, 100% and 99% for CG, and 100% and 100% for TV, and when compared to consensus results. CONCLUSION: The CV/TV and BV assays surpassed the acceptance criteria threshold of 95%, and proved to be an excellent alternative to conventional testing.

Evaluation of the clinical and analytical performance of the Seegene allplex™ SARS-CoV-2 variants I assay for the detection of variants of concern (VOC) and variants of interests (VOI).

BACKGROUND: High-throughput assays for the detection of SARS-CoV-2 variants of concern (VOC) and interest (VOI) are a diagnostic alternative when whole genome sequencing (WGS) is unavailable or limited. OBJECTIVE: This study evaluated the clinical and analytical performance of the Seegene Allplex™ SARS-CoV-2 Variants I assay, which detects the HV69/70 deletion, N501Y and E484K mutations of the S gene. METHODS: Genotyping was evaluated on -871 SARS-CoV-2 RNA positive specimens, 408 nasopharyngeal (NP) swabs and 463 saline gargle (SG) specimens, with WGS used as the reference standard. Analytical performance was assessed including stability, reproducibility, limit of detection (LOD), cross-reactivity and interference with various respiratory microorganisms. RESULTS: The clinical study revealed sensitivity of 100% (95% CI 99.27%-100%) and specificity of 100% (95% CI 98.99%-100%) for HV69/70 deletion, sensitivity of 100% (95% CI 99.55%-100%) and specificity of 100% (95% CI 93.73% - 100%) for N501Y, and sensitivity of 100% (95% CI 98.94% - 100%) and specificity of 98.10% (95% CI 96.53% - 99.08%) for E484K mutation. The E484Q mutation was detected in 10 specimens of the Kappa variant (B.1.627.1). Analytical performance demonstrated stability and reproducibility over 7 days, and LOD was calculated at 698 cp/mL for NP swab specimens, and 968 cp/mL for SG specimens. No interference or cross-reactivity with other microorganisms was noted. CONCLUSION: The Allplex™ SARS-CoV-2 Variants I assay is acceptable for clinical use for the detection of variant of concern and variant of interest.

COVID-19 outbreak in a long-term care facility in Kelowna, British Columbia after rollout of COVID-19 vaccine in March 2021.

BACKGROUND: In March 2021, a coronavirus disease 2019 (COVID-19) outbreak was declared at a large long-term care and short stay facility in British Columbia, Canada-well after introduction of the vaccination program in long-term care facilities that resulted in a dramatic decline in the number of outbreaks in this type of setting. The objective of this study is to provide the descriptive epidemiology of this outbreak, in the context of partial immunization of both residents and staff at the facility. METHODS: The cases' information was extracted from a provincial information system (Panorama). Descriptive analysis was performed using Microsoft Excel and SAS. Outbreak management controls included, but were not limited to, asymptomatic testing and efforts to increase vaccination. RESULTS: Twenty-six cases among the 241 resident and three cases among the 418 staff (corresponding to attack rates of 10% and less than 1%, respectively) were identified. The attack rate in residents was considerably lower than the average attack rate for COVID-19 outbreaks in long-term care facilities before the vaccine rollout. Seventeen resident cases were either partially or fully immunized. Four of the eight hospitalized cases and two of the three deceased cases were partially immunized. Seventeen cases were temporary stay residents. The three staff cases were not vaccinated. Ten cases were identified as part of asymptomatic testing. CONCLUSION: Introduction of vaccination at facilities contributed to lower attack rates and higher numbers of asymptomatic cases in this outbreak. Screening asymptomatic individuals identified additional cases among vaccinated residents. Findings underscore the importance of achieving high vaccine coverage, including among temporary stay residents, to prevent virus introduction and subsequent unrecognized transmission opportunities.

Emergence of Morganellaceae Harboring blaIMP-27 Metalloenzyme in Canada.

In 2018 to 2019, PCR for carbapenemases in routine Gram-negative isolates submitted to the National Microbiology Laboratory revealed an increase in IMP-type metalloenzyme-positive isolates, mostly among Morganellaceae Whole-genome sequencing revealed that 23 Morganellaceae harbored blaIMP-27 within a chromosomal Tn7 element. Phylogenomics indicated diversity of isolates but also the presence of a few clonal isolates dispersed geographically. These isolates may be difficult to detect due to carbapenem susceptibility and false-negative results in phenotypic testing.IMPORTANCE Over the last decade or so, the frequency of isolation of clinical carbapenemase-producing organisms (CPOs) has increased among health care-associated infections. This may seriously compromise antimicrobial therapy, as carbapenems are considered the last line of defense against these organisms. The ability of carbapenemases to hydrolyze most ß-lactams in addition to the co-occurrence of mechanisms of resistance to other classes of antimicrobials in CPOs can leave few options for treating infections. The class B metalloenzymes are globally distributed carbapenemases, and the most commonly found include the NDM, VIM, and IMP types. Our study describes a sudden emergence of IMP-27-harboring Morganellaceae during 2018 to 2019 in Canada. There is a paucity of literature on IMP-27 isolates, and our data bolster the information on the genetic context, antimicrobial profiles, and phylogenomics of this group of CPOs.

Medication error reporting systems: a survey of canadian intensive care units.

BACKGROUND: Patients in the intensive care unit (ICU) have complex problems and experience many medical errors. Currently, little is known about the measurement of medication errors and adverse drug events in Canadian ICUs. OBJECTIVE: To investigate methods of measuring medication errors and adverse drug events in ICUs in Canada. METHODS: A questionnaire was constructed and uploaded to an online survey tool, SurveyMonkey. Through the mailing list software of the Critical Care Pharmacy Specialty Network of the Canadian Society of Hospital Pharmacists, the survey was sent by e-mail to 146 pharmacists working in 79 ICUs across Canada; 2 reminder e-mails followed. The survey was open from July 18 to September 18, 2007. RESULTS: A total of 34 individual responses were received from 31 (39%) of the 79 ICUs. Responses were from academic hospitals (11/31 [35%]), community teaching hospitals (9/31 [29%]), and community nonteaching hospitals (11/31 [35%]). Twenty-six (84%) of the 31 responding ICUs had a process for tracking medication errors and adverse drug events: non-anonymous voluntary reporting (19 or 73%), direct observation (14 or 54%), anonymous voluntary reporting (12 or 46%), chart review (6 or 23%), computerized system (3 or 12%), trigger tools (2 or 8%), pharmacist intervention (2 or 8%), and weekly ICU "safety huddles" (1 or 4%). Fourteen (54%) of the 26 ICUs that had a method of measuring medication errors and adverse drug events had implemented changes to address identified problems. CONCLUSIONS: Most respondents were measuring the frequency of medication errors and adverse drug events, but a wide variety of methods were in use. Only about half of the ICUs had implemented changes as a result of these measurements. There is an opportunity to improve standardization of the measurement of medication errors and adverse drug events in Canadian ICUs.

Incidence of medication errors and adverse drug events in the ICU: a systematic review.

BACKGROUND: Medication errors (MEs) and adverse drug events (ADEs) are both common and under-reported in the intensive care setting. The definitions of these terms vary substantially in the literature. Many methods have been used to estimate their incidence. METHODS: A systematic review was done to assess methods used for tracking unintended drug events in intensive care units (ICUs). Studies published up to 22 June 2007 were identified by searching eight online databases, including Medline. In total, 613 studies were evaluated for inclusion by two reviewers. RESULTS: The authors selected 29 papers to analyse; all studies took place in an ICU, were reproducible and reported ICU-specific rates of events. Rates of MEs varied from 8.1 to 2344 per 1000 patient-days, and ADEs from 5.1 to 87.5 per 1000 patient-days. The definitions of ADE and ME in the studies varied widely. CONCLUSIONS: Much variation exists in reported rates and definitions of ADEs and MEs in ICUs. Some of this variation may be due to a lack of standard definitions for ADEs and MEs, and methods for detecting them. Further standardisation is needed before these methods can be used to evaluate process improvements.

Intensive nursing work schedules and the risk of hypoglycaemia in critically ill patients who are receiving intravenous insulin.

RATIONALE: Nurses in the intensive care unit (ICU) commonly work frequent 12 h shifts, potentially leading to fatigue and reduced vigilance. The authors hypothesised that rates of hypoglycaemia in patients receiving an insulin infusion would be associated with the intensity of work of the bedside nurse in the preceding 72 h. METHODS: The authors identified ICU patients who had hypoglycaemia (glucose ≤3.5 mmol/l, 63 mg/dl) between October 2006 and June 2007. The number of shifts worked in the previous 72 h was calculated for the nurse caring for the patient when the event occurred (case shift). For each case shift, the authors identified up to three control shifts (24, 48 and 72 h before the event in the same patient) and calculated the number of shifts worked by nurses on these shifts in the previous 72 h. Conditional logistic regression was used to determine whether the number of shifts worked was associated with hypoglycaemia. RESULTS: There were 41 events (32 patients). Each additional shift worked in the previous 72 h was associated with a significantly increased risk of hypoglycaemia (OR = 1.65/shift, 95% CI 1.01 to 2.68, p = 0.04) after controlling for nurse age and experience. The association was greater for the 23 events associated with an error in management according to the insulin protocol (OR = 2.93/shift, 1.15 to 7.44, p = 0.02) compared with events not associated with an error (OR = 1.34/shift, 0.73 to 2.45, p = 0.34). CONCLUSIONS: Intensive nursing work schedules are associated with hypoglycaemic events in ICU patients.