Effectiveness of a grid mattress on adults' sleep quality and health: A quasi-experimental intervention study.

Background and aims: Despite that 93% of people indicate that a mattress plays a pivotal role in achieving high-quality sleep, there is a scarcity of research investigating the influence of mattresses on sleep quality, pain, and mood in nonclinical poor sleepers. The purpose was to examine the effectiveness of a pressure-releasing medium-firm grid mattress on sleep and health outcomes (e.g., mood, pain, daytime fatigue) of adults with nonclinical insomnia symptoms using a quasi-experimental design. Methods: Participants were 39 adults (mean age = 45.29) with nonclinical insomnia (i.e., occasional sleeplessness). Following 1 week of baseline assessments on their current mattress, they slept on a pressure-relieving grid mattress for 8 weeks. Participants completed self-report assessments of the Pittsburgh Sleep Quality Index, Berlin Questionnaire, Insomnia Severity Index, Restorative Sleep Questionnaire, Perceived Stress Scale, Profile of Mood States, Daytime Fatigue Scale, Pain and Sleep Questionnaire, and Brief Pain Inventory at Baseline and Weeks 1, 2, 3, 4, and 8. Participants continually wore an Oura Ring to objectively assess sleep and daytime activity. The data were collected from January 2022 to April 2022 and were stored electronically. Repeated-measures analyses of variance were used to analyze mean time differences. Results: Self-reported sleep quality, perceived pain, perceived stress, mood, and daytime fatigue improved significantly from Baseline to Week 8, p's < 0.05. Objective Oura Ring validated the self-reported sleep and daytime activity outcomes with improvements in sleep duration, time awake during the night, light sleep, deep sleep, and total sleep time, p's < 0.05. No significant time effects were evidenced for rapid eye movement sleep. No adverse events were reported. Conclusion: The grid mattress is a simple, noninvasive, and nonpharmacological intervention that improved adults sleep quality and health. Controlled trials are encouraged to examine the effects of this mattress in a variety of populations and environments.

Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing.

Omicron has become the dominant SARS-CoV-2 variant globally since December 2021, with distinct waves being associated with separate Omicron sublineages. Rapid detection of BA.1, BA.2, BA.4, and BA.5 was accomplished in the province of Alberta, Canada, through the design and implementation of real-time reverse transcriptase PCR assays targeting S:N501Y, S:ins214EPE, S:H69/V70, ORF7b:L11F, and M:D3N. Using the combination of results for each of these markers, samples could be designated as belonging to sublineages within BA.1, BA.2, BA.4, or BA.5. The analytical sensitivity of these markers ranged from 132 to 2229 copies/mL and in-laboratory accuracy was 98.9-100%. A 97.3% agreement using 12,592 specimens was demonstrated for the assays compared to genome sequencing. The use of these assays, combined with genome sequencing, facilitated the surveillance of SARS-CoV-2 lineages throughout a BA.5-dominated period.

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.

Evolving strategy for an evolving virus: Development of real-time PCR assays for detecting all SARS-CoV-2 variants of concern.

In order to detect the SARS-CoV-2 variants of concern (VOCs), five real-time reverse transcriptase PCR (rRT-PCR) assays were designed to target the critical discriminatory mutations responsible for the following amino acid changes in the spike protein: two Δ69-70 + N501Y + E gene triplexes (one optimized for Alpha [B.1.1.7] and one optimized for Omicron [B.1.1.529]), a K417N + 242-244 wild-type duplex, a K417T + E484K duplex, and a L452R + P681 + E484Q triplex. Depending on the assay, sensitivity was 98.97-100% for the detection of known VOC-positive samples, specificity was 97.2-100%, limit of detection was 2-116 copies/reaction, intra- and interassay variability was less than 5%, and no cross-reactivity with common respiratory pathogens was observed with any assay. A subset of rRT-PCR- positive VOC samples were further characterized by genome sequencing. A comparison of the lineage designation by the VOC rRT-PCR assays and genome sequencing for the detection of the Alpha, Beta, Gamma, Delta and Omicron variants showed clinical sensitivities of 99.97-100 %, clinical specificities of 99.6-100 %, positive predictive values of 99.8-100%, and negative predictive values of 99.98-100 %. We have implemented these rRT-PCR assays targeting discriminatory single nucleotide polymorphisms for ongoing VOC screening of SARS-CoV-2 positive samples for surveillance purposes. This has proven extremely useful in providing close to real-time molecular surveillance to monitor the emergence of Alpha, the replacement of Alpha by Delta, and the replacement of Delta by Omicron. While the design, validation and implementation of the variant specific PCR targets is an ever-evolving approach, we find the turn-around-time, high throughput and sensitivity to be a useful complementary approach for SARS-CoV-2 genome sequencing for surveillance purposes in the province of Alberta, Canada.

Precision Response to the Rise of the SARS-CoV-2 B.1.1.7 Variant of Concern by Combining Novel PCR Assays and Genome Sequencing for Rapid Variant Detection and Surveillance.

SARS-CoV-2 variants of concern (VOCs) have emerged as a global threat to the COVID-19 pandemic response. We implemented a combined approach to quickly detect known VOCs while continuously monitoring for evolving mutations of the virus. To rapidly detect VOCs, two real-time reverse transcriptase PCR assays were designed and implemented, targeting the spike gene H69/V70 deletion and the N501Y mutation. The H69/V70 deletion and N501Y mutation assays demonstrated accuracies of 98.3% (95% CI 93.8 to 99.8) and 100% (95% CI 96.8 to 100), limits of detection of 1,089 and 294 copies/ml, and percent coefficients of variation of 0.08 to 1.16% and 0 to 2.72% for the two gene targets, respectively. No cross-reactivity with common respiratory pathogens was observed with either assay. Implementation of these tests allowed the swift escalation in testing for VOCs from 2.2% to ∼100% of all SARS-CoV-2-positive samples over 12 January to 9 February 2021, and resulted in the detection of a rapid rise of B.1.1.7 cases within the province of Alberta, Canada. A prospective comparison of the VOC assays to genome sequencing for the detection of B.1.1.7, combined detection of P.1 and B.1.351, and wild-type (i.e., non-VOC) lineages showed sensitivities of 98.2 to 100%, specificities of 98.9 to 100%, positive predictive values of 76.9% to 100%, and negative predictive values of 96 to 100%. Variant screening results inform sampling strategies for regular surveillance by genome sequencing, thus allowing rapid identification of known VOCs while continuously monitoring the evolution of SARS-CoV-2 in the province. IMPORTANCE Different strains, or variants, of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus that causes COVID-19) have emerged that have higher levels of transmission, less susceptibility to our immune response, and possibly cause more severe disease than previous strains of the virus. Rapid detection of these variants of concern is important to help contain them and prevent them from spreading widely within the population. This study describes two newly developed tests that are able to identify and differentiate the variants of concern from regular strains of SARS-CoV-2. These tests are faster and simpler than the main, gold standard method of identifying variants of concern (genome sequencing). These tests also demonstrated a high correlation with genome sequencing and allowed for the rapid and accurate detection of the rise of B.1.1.7 (one of the variants of concern) in the province of Alberta, Canada.

Effect of a Free-Living Ketogenic Diet on Feasibility, Satiety, Body Composition, and Metabolic Health in Women: The Grading Level of Optimal Carbohydrate for Women (GLOW) Study.

OBJECTIVE: The study's purpose was to examine a free-living, ketogenic diet (WFKD) on feasibility, satiety, body composition, and metabolic health in women. METHODS: Twenty-two women (age (yr.) 42.2 ± 8.1, Ht. (cm) 164.2 ± 5.9, BMI 27.3 ± 6.0) participated in a 21-day, free-living dietary intervention. Daily ketone measurements and satiety/craving surveys, weekly diet records, and PRE and POST assessments of anthropometrics, body composition, blood pressure, and fasted capillary-blood glucose (BG) and cholesterol panels were collected. RESULTS: Women maintained calories (PRE: 1938 kcal vs POST: 1836 kcal) and protein (PRE: 17% vs POST: 20%) but decreased carbohydrate (PRE: 36% vs POST: 13%) and increased fat (PRE: 45% vs POST: 65%) PRE to POST (p ≤ 0.05). Daily self-reports suggested no changes in satiety or food cravings between PRE, WK 1, WK 2, and WK 3. Ketones increased (PRE 0.3 ± 0.2 mmol vs POST 0.8 ± 0.6 mmol) PRE to POST with significant differences between PRE and all other time points (p ≤ 0.05). Bodyweight (PRE: 73.9 kg vs POST: 72.3 kg) and body fat (PRE: 28.9 ± 13.4 kg vs POST 27. 4 ± 13.5 kg) decreased but there were no differences in fat-free mass PRE to POST (p ≤ 0.05). Systolic blood pressure decreased (PRE: 119.2 ± 8.9 mmHg vs POST: 109.5 ± 10.9 mmHg), diastolic blood pressure increased (PRE: 74.1 ± 7.5 mmHg vs POST: 78.8 ± 7.4 mmHg), and BG improved (94.0 ± 8.3 mg/dL vs POST 89.9 ± 9.0 mg/dL) PRE to POST (p ≤ 0.05). No differences were observed in total cholesterol (TC), high-density lipoprotein (HDL), and triglycerides (TG) but TC/HDL decreased and low-density lipoprotein increased PRE to POST (p ≤ 0.05). CONCLUSION: Women were able to maintain calories, improve body composition, blood pressure, and BG, increase ketones, and improve some but not all cholesterol markers after 21 days on a free-living WFKD.

Spatial distribution of Escherichia coli ST131 C subclades in a centralized Canadian urban region.

INTRODUCTION: Escherichia coli ST131 is the most common multidrug-resistant (MDR) E. coli clone causing bloodstream infections (BSIs) in Calgary. This study describes patient characteristics and spatial distribution of ST131 subclades C1 and C2 causing BSIs in Calgary. METHODS: E. coli from blood (n = 685) obtained in Calgary, Canada, (2016) were PCR screened for ST131 and positives (n = 141) underwent whole genome sequencing. Patient characteristics were analysed using Fisher's Exact/t-tests and spatial analysis was used to identify clusters. RESULTS: Overall, 21% of E. coli was identified as ST131 and clade C dominated the population. ST131-C2 was associated with blaCTX-M-15 and significantly more MDR than ST131-C1. The spatial distribution in Calgary showed that ST131-C1 was mainly present in long-term care (LTC) residents whereas ST131-C2 clustered in a specific North East (NE) Calgary sector comprising of six neighbourhoods without LTC centres. This NE sector has high immigration and travel rates from the Indian subcontinent. CONCLUSIONS: This study showed that ST131 C subclades have different geographical distribution patterns in Calgary. We believe that recent travel to and immigration from certain high-risk regions for antimicrobial resistance are responsible for the ST131-C2 NE Calgary clustering pattern.

Trends in Population Dynamics of Escherichia coli Sequence Type 131, Calgary, Alberta, Canada, 2006-20161.

Global expansion of antimicrobial drug-resistant Escherichia coli sequence type (ST) 131 is unrivaled among human bacteria. Understanding trends among ST131 clades will help with designing prevention strategies. We screened E. coli from blood samples (n = 1,784) obtained in Calgary, Alberta, Canada, during 2006, 2012, and 2016 by PCR for ST131 and positive samples (n = 344) underwent whole-genome sequencing. The incidence rate per 100,000 residents increased from 4.91 during 2006 to 12.35 during 2012 and 10.12 during 2016. ST131 belonged to clades A (10%), B (9%), and C (81%). Clades C1-nonM27 and B were common during 2006, and C2 containing blaCTX-M-15, C1-M27 containing blaCTX-M-27, and A were responsible for the increase of ST131 during 2012 and 2016. C2 was the most antimicrobial drug-resistant subclade and increased exponentially over time. Eradicating ST131, more specifically the C2 subclade, will lead to considerable public health benefits for persons in Calgary.

Effectiveness of NexQuest Natural Frequency Technology® on sleep and mood of adults with insomnia symptoms: a randomized, double blind and placebo controlled crossover trial.

OBJECTIVES: The study purpose was to conduct a four-week randomized double-blind placebo-controlled crossover trial on adults with insomnia symptoms to examine the effectiveness of Natural Frequency Technology(®) (NFT), found in Philip Stein Sleep Bracelets, on sleep quality, anxiety/stress levels, and mood. METHODS: Adults (N = 44, M age = 41.9 years) were randomized to the Placebo Bracelet (PB) or NFT Sleep Bracelet (SB) for two weeks and then the alternative bracelet for two weeks. Self-reported mood, anxiety/stress, and sleep quality were completed at Day 0 (PRE) and following each condition; POST PB and POST SB). RESULTS: When the participants wore the SB, compared to the PB, they had improved sleep quality (i.e., Pittsburgh Sleep Quality Index), anxiety/perceived stress, and mood, p's < .05. DISCUSSION: The SB may be simple, noninvasive, and non-pharmacological intervention to improve sleep quality and daytime mood.

A Comprehensive Account of Escherichia coli Sequence Type 131 in Wastewater Reveals an Abundance of Fluoroquinolone-Resistant Clade A Strains.

In the ten years since its discovery, the Escherichia coli clone sequence type 131 (ST131) has become a major international health threat, with the multidrug-resistant and extended-spectrum ß-lactamase (ESBL)-producing clade C emerging as the globally dominant form. ST131 has previously been isolated from wastewater; however, most of these studies selectively screened for ESBL-producing organisms, thereby missing the majority of remaining ST131 clades. In this study, we used a high-throughput PCR-based screening strategy to comprehensively examine wastewater for the presence of ST131 over a 1-year period. Additional multiplex PCRs were used to differentiate clades and obtain an unbiased account of the total ST131 population structure within the collection. Furthermore, antimicrobial susceptibility profiles of all ST131-positive samples were tested against a range of commonly used antibiotics. From a total of over 3,762 E. coli wastewater samples, 1.86% (n = 70) tested positive for ST131, with the majority being clade A isolates. In total, 63% (n = 44) were clade A, 29% (n = 20) were clade B, 1% (n = 1) were clade C0, 6% (n = 4) were clade C1, and 1% (n = 1) were clade C2. In addition, a very high rate of resistance to commonly used antibiotics among wastewater isolates is reported, with 72.7% (n = 32) of clade A resistant to ciprofloxacin and high rates of resistance to gentamicin, sulfamethoxazole-trimethoprim, and tetracycline in clades that are typically sensitive to antibiotics.IMPORTANCE ST131 is a global pathogen. This clone causes urinary tract infections and is frequently isolated from human sources. However, little is known about ST131 from environmental sources. With the widely reported increase in antibiotic concentrations found in wastewater, there is additional selection pressure for the emergence of antibiotic-resistant ST131 in this niche. The unbiased screening approach reported herein revealed that previously antibiotic-sensitive lineages of ST131 are now resistant to commonly used antibiotics present in wastewater systems and may be capable of surviving UV sterilization. This is the most comprehensive account of ST131 in the wastewater niche to date and an important step in better understanding the ecology of this global pathogen.

Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada.

We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, and O157. We also report draft assemblies, with standardized metadata, for 360 STEC strains isolated from watersheds, animals, farms, food, and human infections.

Molecular Diagnosis of Vaginitis: Comparing Quantitative PCR and Microbiome Profiling Approaches to Current Microscopy Scoring.

Vaginitis is often diagnosed by microscopy and limited to testing for bacterial vaginosis (BV), vulvovaginal candidiasis, and trichomoniasis. Approximately 10% of vaginal swabs are negative but designated "altered flora" by BV Nugent score, leaving clinicians unsure how to treat patients. Accurate and comprehensive vaginitis diagnostics are needed to direct treatment and reduce risks of recurrent or more severe infections. Vaginal swabs were collected from 93 women (mean age, 23.53 years; range, 18 to 42 years) in a cross-sectional study. Microscopy results for BV and Candida were compared to those from two molecular approaches: (i) a comprehensive quantitative PCR (qPCR) assay, including testing for aerobic vaginitis (AV), Candida, sexually transmitted infections (STI), and BV (Applied Biosystems) with an accompanying BV interpretive algorithm (Coriell Life Sciences), and (ii) microbiome profiling of the 16S rRNA gene (Illumina). Microscopy plus BV Nugent score had 76% overall agreement with the qPCR plus BV interpretive algorithm method (24 positive, 47 negative). OF the nine samples designated altered flora by Nugent, five were categorized BV positive and four were BV negative by the qPCR method. Although BV negative, 3/4 of the latter samples had positive AV targets with one also was STI positive. Microscopic identification of Candida versus that by qPCR had 94% agreement (9 positive, 78 negative). The comprehensive qPCR assay revealed alternative etiologies summarized as 38% BV, 10% AV, 5% Candida, 2% STI, 10% mixed infection (positive targets in multiple panels), and 35% negative for all targets. 16S microbiome analysis confirmed the bacterial qPCR results and identified differentiating patterns between AV, BV, and Lactobacillus-dominated vaginal microbiomes.

JAK2-tree: a simple CBC-based decision rule to guide appropriate JAK2 V617F mutation testing.

AIMS: The JAK2 V617F mutation is highly recurrent in many of the myeloproliferative neoplasms, a molecular variant that can be easily detected using sensitive and minimally invasive techniques. Given the ease of JAK2 V617F testing, this test may be improperly requested for the purposes of patient 'screening' and to optimise laboratory resource utilisation, it behooves clinicians and laboratorians to perform JAK2 V617F testing only when most appropriate. METHODS: To assist with the screening of patients being considered for JAK2 V617F testing, we developed a clinical decision rule, "JAK2-tree", which can be easily applied to basic CBC parameters (haemoglobin, platelet and white blood cell counts). RESULTS: We tested JAK2-tree on two independent datasets, one an unselected population-based sample (the Copenhagen General Population Study) and the other an historical clinical laboratory referral set, with sensitivities for JAK2 V617F detection of 91% and 94%, respectively. As applied to the historical laboratory referral dataset, moreover, the JAK2-tree algorithm would have reduced JAK2 V617F testing volume over the period of evaluation by 15%. CONCLUSIONS: Our work supports a simple decision-tree-based screening approach to optimize the selection of patients most appropriate for JAK2 V617F testing.

Efficacy of Wholetones® 2Sleep and classical music on sleep and health behaviors of adults with insomnia symptoms: A single blind, randomized, controlled, crossover pilot trial.

OBJECTIVES: To conduct a randomized single-blind placebo-controlled crossover trial on adults with insomnia symptoms to examine the efficacy of Wholetones® 2Sleep Music (WM) and Classical Music (CM) on sleep quality, anxiety/stress, fatigue, productivity, and mood. METHODS: Following baseline assessments, 38 adults (M age = 46.6 years) were randomized to either WM or CM conditions for 10 days and then the alternative music for 10 days after a 4 day "wash-out". The outcomes were sleep quality (i.e., Pittsburgh Sleep Quality Index) and psychological measures. RESULTS: Listening to both the WM and CM resulted in significant improvements from baseline for sleep quality, stress/anxiety, fatigue, productivity, and mood (p<0.05). CONCLUSION: WM and CM provides a simple, noninvasive, and non-pharmacological intervention to promote sleep quality resulting in improved daytime mood, fatigue, productivity, and anxiety/stress.

Reporting on the prevalence of antiretroviral drug resistance in a regional HIV population over 20 years: a word of caution.

BACKGROUND: Failure to achieve complete viral suppression with antiretroviral drugs (ARV) may lead to uncontrolled HIV replication, ARV resistance and negative outcomes. Monitoring and reporting of HIV resistance trends is important but problematic. We examined prevalent resistance rates in an HIV population over 20 years and document how rates may appear to vary greatly based solely on which parameters are utilized. METHODS: We determined the annual use of genotypic antiretroviral resistance testing (GART) from 1995 to 2014 for all patients receiving HIV care in southern Alberta, Canada, and the presence of resistance mutations in those tested. The impact on prevalent resistance rates of using cumulative or latest GART was also determined. RESULTS: Between 1995 and 2014, the number of patients with GART increased from <1% to 71%. Prevalent resistance in patients with GART decreased from a high of 52% in 2003 to 25.8% in 2014. However, if prevalence rates were reported using all active patients as denominator, including those without GART, prevalence increased from 0.7% to 18.5%. Prevalence rates were 7% to 9% higher in any given year if cumulative GART rather than latest GART results were used. CONCLUSIONS: While prevalence resistance rates are decreasing, the precise rates being reported may vary due to increasing number of patients tested annually, using either the entire population as denominator or only patients with GART, and using either last or cumulative GART. Defining these parameters is critical if prevalence is to be compared over time or between HIV populations.

Complete Sequencing of Plasmids Containing blaOXA-163 and blaOXA-48 in Escherichia coli Sequence Type 131.

OXA-48-like enzymes have emerged as important extended-spectrum ß-lactamases/carbapenemases in Escherichia coli sequence type 131 (ST131). We report the structures of the first fully sequenced blaOXA-163 plasmid and of two other blaOXA-48 plasmids in this lineage. blaOXA-163 was located on a 71-kb IncN plasmid with other resistance genes. blaOXA-48 was present on IncL/M plasmids, genetically similar to other blaOXA-48 plasmid sequences, and consistent with interspecies/interlineage spread. The presence of blaOXA-48-like genes on epidemic plasmids in ST131 is of concern.

Molecular Evolution of a Klebsiella pneumoniae ST278 Isolate Harboring blaNDM-7 and Involved in Nosocomial Transmission.

During 2013, ST278 Klebsiella pneumoniae with blaNDM-7 was isolated from the urine (KpN01) and rectum (KpN02) of a patient in Calgary, Canada. The same strain (KpN04) was subsequently isolated from another patient in the same unit. Interestingly, a carbapenem-susceptible K. pneumoniae ST278 (KpN06) was obtained 1 month later from the blood of the second patient. Next-generation sequencing (NGS) revealed that the loss of carbapenem-resistance in KpN06 was due to a 5-kb deletion on the blaNDM-7-harboring IncX3 plasmid. In addition, an IncFIB plasmid in KpN06 had a 27-kb deletion that removed genes encoding for heavy metal resistance. Phylogenetic analysis showed that the K. pneumoniae ST278 from patient 2 was likely a descendant of KpN02 and that KpN06 was a close progenitor of an environmental ST278. It is unclear whether KpN06 lost the blaNDM-7 gene in vivo. This study detailed the remarkable plasticity and speed of evolutionary changes in multidrug-resistant K. pneumoniae, demonstrating the highly recombinant nature of this species. It also highlights the ability of NGS to clarify molecular microevolutionary events within antibiotic-resistant organisms.

First Report of blaIMP-14 on a Plasmid Harboring Multiple Drug Resistance Genes in Escherichia coli Sequence Type 131.

The blaIMP-14 carbapenem resistance gene has largely previously been observed in Pseudomonas aeruginosa and Acinetobacter spp. As part of global surveillance and sequencing of carbapenem-resistant Escherichia coli, we identified a sequence type 131 strain harboring blaIMP-14 within a class 1 integron, itself nested within an ∼54-kb multidrug resistance region on an epidemic IncA/C2 plasmid. The emergence of blaIMP-14 in this context in the ST131 lineage is of potential clinical concern.

Maintaining the continuity of HIV-care records for patients transferring care between centers: challenges, workloads, needs and risks.

With improved life expectancy, the medical records of HIV-infected patients are likely to be transferred repeatedly between HIV caregivers. The challenges, and risk for introducing medical error from incomplete record transfers are poorly understood. We measured number of requests for record transfer, the workload incurred, and explore, using genotypic antiretroviral resistance testing results (GART), the potential risk of incomplete records. Using retrospective database and chart review, we examined all patients followed at the Southern Alberta Clinic between 1 January 2004 and 1 January 2015, and determined how many patients transferred care into and out our program, the associated requests and the workload for record transfer. Using a complete record of all GART tests, the potential importance of absent historic records in current treatment decisions was analyzed. The annual churn rate was 22 ± 3.4%. We received requests for only 70% of patient records who had left our care. Median time for receipt of incoming medical records was 28 days; average clerical time for processing data was 2 hours/record. Of all GART results, 25% exhibited resistance. Of 111 patients with potentially misleading GART results (i.e., documented historical resistance not visible on more recent GART), 34 (30.6%) had moved in from elsewhere. Rigorous maintenance of the continuity of the HIV record is not universally practiced. Resources, costs and logistic challenges as well as a lack of appreciation of risks clearly shown by GART testing, may be relevant barriers. Addressing such issues is pressing as aging and transfers of care are increasingly common.

A Primer on Infectious Disease Bacterial Genomics.

The number of large-scale genomics projects is increasing due to the availability of affordable high-throughput sequencing (HTS) technologies. The use of HTS for bacterial infectious disease research is attractive because one whole-genome sequencing (WGS) run can replace multiple assays for bacterial typing, molecular epidemiology investigations, and more in-depth pathogenomic studies. The computational resources and bioinformatics expertise required to accommodate and analyze the large amounts of data pose new challenges for researchers embarking on genomics projects for the first time. Here, we present a comprehensive overview of a bacterial genomics projects from beginning to end, with a particular focus on the planning and computational requirements for HTS data, and provide a general understanding of the analytical concepts to develop a workflow that will meet the objectives and goals of HTS projects.