bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome sequencing for antimicrobial surveillance: species-specific quality thresholds and data evaluation from the network of the European Union Reference Laboratory for Antimicrobial Resistance genomic proficiency tests of 2021 and 2022
Authors: Sørensen Lauge Holm , Pedersen Susanne Karlsmose , Jensen Jacob Dyring , Lacy-Roberts Niamh , Andrea Athina , S. M. Brouwer Michael , Veldman Kees T. , Lou Yan , Hoffmann Maria , S. Hendriksen Rene 
Published: August 2024

ABSTRACT

As antimicrobial resistance (AMR) surveillance shifts to genomics, ensuring the quality of whole-genome sequencing (WGS) data produced across laboratories is critical. Participation in genomic proficiency tests (GPTs) not only increases individual laboratories' WGS capacity but also provides a unique opportunity to improve species-specific thresholds for WGS quality control (QC) by repeated resequencing of distinct isolates. Here, we present the results of the EU Reference Laboratory for Antimicrobial Resistance (EURL-AR) network GPTs of 2021 and 2022, which included 25 EU national reference laboratories (NLRs). A total of 392 genomes from 12 AMR-bacteria were evaluated based on WGS QC metrics. Two percent (
n
= 9) of the data were excluded, due to contamination, and 11% (
n
= 41) of the remaining genomes were identified as outliers in at least one QC metric and excluded from computation of the adjusted QC thresholds (AQT). Two QC metric correlation groups were identified through linear regression. Eight percent (
n
= 28) of the submitted genomes, from 11 laboratories, failed one or more of the AQTs. However, only three laboratories (12%) were identified as underperformers, failing across AQTs for uncorrelated QC metrics in at least two genomes. Finally, new species-specific thresholds for “N50” and “number of contigs > 200 bp” are presented for guidance in routine laboratory QC. The continued participation of NRLs in GPTs will reveal WGS workflow flaws and improve AMR surveillance data. GPT data will continue to contribute to the development of reliable species-specific thresholds for routine WGS QC, standardizing sequencing data QC and ensure inter- and intranational laboratory comparability.

IMPORTANCE
Illumina next-generation sequencing is an integral part of antimicrobial resistance (AMR) surveillance and the most widely used whole-genome sequencing (WGS) platform. The high-throughput, relative low-cost, high discriminatory power, and rapid turnaround time of WGS compared to classical biochemical methods means the technology will likely remain a fundamental tool in AMR surveillance and public health. In this study, we present the current level of WGS capacity among national reference laboratories in the EU Reference Laboratory for AMR network, summarizing applied methodology and statistically evaluating the quality of the obtained sequence data. These findings provide the basis for setting new and revised thresholds for quality metrics used in routine WGS, which have previously been arbitrarily defined. In addition, underperforming participants are identified and encouraged to evaluate their workflows to produce reliable results.
Impact of mitigating obesity, smoking, and physical inactivity on type 2 diabetes mellitus burden in Oman: insights from mathematical modeling
Authors: Alareeki Asalah , Awad Susanne F , Al-Mawali Adhra , Morsi Magdi , Critchley Julia A , Al-Lawati Jawad A , Abu-Raddad Laith J 
Published: August 2024

IntroductionTo estimate the impact of reducing obesity, smoking, and physical inactivity (PIA) prevalence, and of introducing physical activity (PA) as an explicit intervention, on the prevalence, incidence, and mortality of type 2 diabetes mellitus (T2DM) in Oman.Research design and methodsA deterministic population-level mathematical model was employed to investigate the impact of different scenarios for reducing T2DM risk factors on T2DM epidemiology. The model was stratified by sex, age group, risk factor status, T2DM status, and intervention status and parameterized with nationally representative data. Intervention scenarios were calculated and compared with a baseline (no-intervention) scenario for changes in T2DM prevalence, incidence, and mortality among adult Omanis between 2020 and 2050.ResultsIn the no-intervention scenario, T2DM prevalence increased from 15.2% in 2020 to 23.8% in 2050. Achieving the goals of halting the rise of obesity, reducing smoking by 30%, and reducing PIA by 10% as outlined in the WHO’s Global Action Plan for Non-communicable Diseases (implemented between 2020 and 2030 and then maintained between 2031 and 2050) would reduce T2DM prevalence by 32.2%, cumulative incidence by 31.3%, and related deaths by 19.3% by 2050. Halting the rise of or reducing obesity prevalence by 10%–50% would reduce T2DM prevalence by 33.0%–51.3%, cumulative incidence by 31.9%–53.0%, and related deaths by 19.5%–35.6%. Reducing smoking or PIA prevalence by 10%–50% would lead to smaller reductions of less than 5% in T2DM prevalence, cumulative incidence, and related deaths. Introducing PA with varying intensities at a 25% coverage would reduce T2DM prevalence by 4.9%–14.1%, cumulative incidence by 4.8%–13.8%, and related deaths by 3.4%–9.6% by 2050.ConclusionsIntervention-for-prevention efforts targeting obesity reduction and introducing PA could result in major reductions in the T2DM burden. Prioritizing such interventions could alleviate the burden of T2DM in Oman and other countries with similarly high T2DM and obesity burdens.
Changes in use and hospital outcomes of bariatric surgery in Spain (2016–2022): analysis of the role of type 2 diabetes using propensity score matching
Authors: Lopez-de-Andres Ana , Jimenez-Garcia Rodrigo , Cuadrado-Corrales Natividad , Carabantes-Alarcon David , Hernandez-Barrera Valentin , de Miguel-Diez Javier , Jimenez-Sierra Ana , Zamorano-Leon José Javier 
Published: August 2024

IntroductionThe objectives of this study were to examine temporal trends in the incidence of bariatric surgery (Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG)) in patients with and without type 2 diabetes mellitus (T2DM). Outcomes of hospitalization and the impact of T2DM on these outcomes were also analyzed.Research design and methodsWe performed an observational study with the Spanish national hospital discharge database. Obese patients with and without T2DM who underwent RYGB and SG between 2016 and 2022 were identified. Propensity score matching (PSM) and logistic regression were used to compare patients with and without T2DM and to evaluate the effect of T2DM and other variables on outcomes of surgery. A variable “severity” was created to cover patients who died in hospital or were admitted to the intensive care unit (ICU).ResultsA total of 32,176 bariatric surgery interventions were performed (28.86% with T2DM). 31.57% of RYGBs and 25.53% of SG patients had T2DM. The incidence of RYGB and SG increased significantly between 2016 and 2022 (p<0.001), with a higher incidence in those with T2DM than in those without (incidence rate ratio 4.07 (95% CI 3.95 to 4.20) for RYGB and 3.02 (95% CI 2.92 to 3.14) for SG). In patients who underwent SG, admission to the ICU and severity were significantly more frequent in patients with T2DM than in those without (both p<0.001). In the multivariate analysis, having T2DM was associated with more frequent severity in those who received SG (OR 1.23; 95% CI 1.07 to 1.42).ConclusionsBetween 2016 and 2022, bariatric surgery procedures performed in Spain increased in patients with and without T2DM. More interventions were performed on patients with T2DM than on patients without T2DM. RYGB was the most common procedure in patients with T2DM. The presence of T2DM was associated with more severity after SG.
Trends in colorectal cancer surgical resection rates during the screening era: a retrospective study in Italy
Authors: Zorzi Manuel , Calciano Lucia , Gennaro Nicola , Memo Laura , Rizzato Silvia , Stocco Carmen , Urso Emanuele D L , Negro Silvia , Spolverato Gaya , Pucciarelli Salvatore , Sbaraglia Marta , Guzzinati Stefano 
Published: August 2024

BackgroundFaecal immunochemical test (FIT)-based screening is effective in reducing colorectal cancer (CRC) incidence, but its sensitivity for proximal lesions remains low.ObjectivesWe compared age-adjusted CRC surgical resection rates across anatomic sites (proximal colon, distal colon, rectum), age groups and sex over 20 years in a large Italian population. We particularly focused on changes in trends following FIT-screening implementation in the target population (50–69 years).DesignThis retrospective study analysed data from the Veneto Region’s administrative Hospital Discharge Dataset, involving over 54 000 patients aged 40–89 (43.4% female) who underwent CRC surgery between 2002 and 2021.ResultsOverall, surgery rates increased until 2007 (annual percentage changes: 2.5% in males, 2.9% in females) and then declined (−4.2% in males, −3.4% in females). This decline was steeper for distal and rectal cancers compared with proximal cancer, suggesting a shift towards more right-sided CRC surgery.In males, the prescreening increase in proximal surgery was reversed after screening implementation (slope change: −6%) while the prescreening decline accelerated for distal (−4%) and rectal (−3%) surgeries. In females, stable prescreening trends shifted downward for all sites (−5% for proximal, −8% for distal and −7% for rectal surgery). However, the change in trends between prescreening and postscreening periods was not different across anatomic sites for either sex (all slope change differences in pairwise comparisons were not statistically significant).ConclusionThe shift towards proximal surgery may not be entirely due to the FIT’s low sensitivity but may reflect an underlying upward trend in proximal cancers independent of screening.
Functional seizures and their mimics: a retrospective service review of cases from a tertiary video telemetry database
Authors: Dudley Peter , Marquez Jan Paul , Farrell Fiona , Benson Jennifer , Rugg-Gunn Fergus , Sidhu Meneka K , O'Sullivan Suzanne , Walker Matthew , Yogarajah Mahinda 
Published: August 2024

ObjectiveIdentify the proportion of patients referred with putative functional seizures (FS) that were subsequently re-diagnosed as epileptic seizures (ES), or an alternative diagnosis, following video telemetry EEG (VTEEG). In addition, describe the characteristics of those seizures.MethodsThe VTEEG reports from patients admitted to the Chalfont Centre for Epilepsy between 2019 and 2022 were reviewed. Pre-VTEEG and post-VTEEG diagnoses were compared to identify whether a diagnostic revision was made from suspected FS to ES or another diagnosis. Diagnostic revision cases were then grouped into cohorts with associated features and reviewed to characterise and describe FS mimics.Results444 VTEEG reports where patients had habitual events were identified. 4.7% of patients were referred with FS and were subsequently diagnosed with ES or another diagnosis. In this group, several cohorts could be identified including frontal lobe epileptic seizures, ES with functional overlay, insular or temporal lobe epileptic seizures associated with autonomic or marked experiential peri-ictal symptoms, and individuals who had both ES and FS but whose ES were revealed on medication withdrawal.ConclusionIn patients referred to a tertiary epilepsy unit, a small minority of cases had seizures diagnosed as functional and reclassified as epileptic or an alternative diagnosis. It is clinically important to be aware of these FS mimics.
Primary care providers’ perspectives on referrals to the Diabetes Prevention Programme: a qualitative comparative study across varied referral patterns
Authors: Stephenson-Hunter Cara , Gonzalez Christopher J , Franco Stacey , Hashmi Maryam , Tisor Ochuwa , Gonzalez Cristina M 
Published: August 2024

IntroductionDespite the effectiveness of Diabetes Prevention Programmes (DPP) in reducing diabetes risk, primary care provider (PCP) referrals remain low, especially among men and racial/ethnic minorities, exacerbating their under-representation in DPPs. Understanding PCPs’ perspectives on referrals is crucial for enhancing the intervention’s reach and effectiveness.Research design and methodsWe conducted a qualitative study to explore PCPs’ experiences, perspectives and engagement with DPP referrals, focusing on factors influencing variations in referral rates. Based on electronic record data, high and low-referring PCPs from a large integrated health system in the Bronx, NY, participated in interviews conducted between February and September 2023. Interviews were conducted and recorded on Zoom, anonymised, transcribed and analysed using the constant comparative method.ResultsFrom 22 PCP interviews, 4 themes emerged representing factors that influenced referrals: (1) perceived barriers to the patient engagement with the DPP, including infrastructure gaps, programme accessibility issues and unmet social needs, particularly affecting low-referring PCPs; (2) perceived effectiveness of the DPP, with concerns raised about its efficacy, especially for male and socioeconomically disadvantaged patients; (3) perceived self-efficacy in referring patients, driven by knowledge gaps and limited opportunities, especially among low-referrers and (4) recommendations to facilitate and strengthen referrals, highlighting areas for PCP and patient support. The perspectives of high-referring/low-referring PCPs often differed across these themes and associated subthemes.ConclusionsOur research illuminates the challenges PCPs face in treating prediabetic patients and factors influencing DPP referrals in underserved populations. This understanding can guide interventions to enhance equitable DPP referrals and engagement, thereby reducing diabetes risk in vulnerable populations.
Surveillance of antibiotics use in inpatients at Benjamin Mkapa Zonal Referral Hospital in Dodoma, Tanzania: a point prevalence survey
Authors: Zimbwe Kauke Bakari , Yona Yusto Julius , Chiwambo Charity Alphonce , Chandika Alphonce Bilola , Kiwelu Humphrey Sawira , Kizenga Omary Salim , Mleke Mfaume Michael , Shabani Moshi Moshi 
Published: August 2024

ObjectiveTo assess antibiotics prescribing and use patterns for inpatients at Benjamin Mkapa Zonal Referral Hospital (BMH) using the WHO-Point Prevalence Survey (WHO-PPS).DesignA cross-sectional survey.SettingThe Benjamin Mkapa Zonal Referral Hospital, Dodoma, Tanzania.ParticipantsInpatient prescriptions, regardless of whether antibiotics were prescribed (n=286) on the day of PPS.Outcome measuresOur study analysed the prevalence of antibiotic use at BMH for inpatients, the type of antibiotics used, the indications for use and the proportion of oral and parenteral antibiotics. We also assessed prescription-prescribed antibiotics after a positive antimicrobial susceptibility testing (AST) result.ResultsA survey was conducted on 286 prescriptions, which revealed that 30.07% of them included antibiotics. On average, each prescription contained at least 1.6 antibiotics. All prescriptions that included antibiotics were written in generic names, and 77.91% (67/86) of them followed the Standard Treatment Guidelines. Of the prescriptions that included antibiotics, 58.14% (50/86) had a single antibiotic, 20.93% (18/86) had parenteral antibiotics and 79.07% (68/86) had oral antibiotics. Based on AWaRe’s (Access, Watch and Reserve) categorisation of antibiotics, 50% (8/16) were in the Access group, 31.25% (5/16) were in the Watch group, 12.50% (2/16) were in the Reserve group and 6.25% (1/16) were not recommended antimicrobial combinations. Out of 86 prescriptions included antibiotics, only 4.65% showed positive culture growth. However, antibiotics were still prescribed in 29.07% of prescriptions where there was no growth of bacteria, and in 66.28% of prescriptions, antibiotics were prescribed empirically without any requesting of bacteria culture and AST.ConclusionBMH has reduced inpatient Antibiotic Use by half compared with the 2019 WHO-PPS. Adherence to National Treatment Guidelines is suboptimal. Clinicians should use AST results to guide antibiotic prescribing.
Toothbrushing programme in Saudi Arabia ‘TOPS’: a study protocol for a cluster randomised controlled trial in kindergartens, Riyadh
Authors: Almutairi Budur , Conway D , Ross Alastair , Hattan Mohammed , Almogren Fayyad , McMahon Alex D 
Published: August 2024

IntroductionDental caries among children is a major global health problem and is a particular public health challenge in Saudi Arabia. Dental caries cause pain, infection and negatively impact quality of life. As part of population oral health improvement efforts in Saudi Arabia, this project aims to evaluate the effectiveness of a supervised toothbrushing programme in kindergartens.Methods and analysisThis study is a cluster randomised controlled trial. Enrolment began in September 2022, for two academic years (2022–2024) on 20 randomly selected kindergartens in Riyadh. The data collection phase will be completed in September 2024. Ten kindergartens are randomly allocated to supervised toothbrushing and 10 to treatment as usual, which is an annual oral health awareness visit. The primary endpoint will be the worsening of obvious decay experience as measured by decayed (into dentine), missing and filled teeth (d3mft) from baseline to the second year of follow-up. The secondary endpoint will be the increase in the number of teeth affected. A priori subgroups of the region of Riyadh, school type (public, private), child sex and presence/absence of prior decay at baseline, will be analysed. We require 244 evaluable endpoints using a power of 80% to meet the sample size requirement. In addition, questionnaires on behaviours, quality of life, process monitoring and cost analysis are being deployed.Ethics and disseminationEthics approval for this study was given by the King Fahad Medical City Institutional Review Board in the Saudi Ministry of Health (22-083E/March 2022). The data analysis has been approved by the University of Glasgow Medical Veterinary and Life Sciences Research Ethical Committee (200220194/March 2023). The results of this study will be disseminated through presentations at scientific conferences and in scientific journals.Trial registration numberNCT05512156.
Easing the way to achieving target serum urate in people with gout: protocol for a non-inferiority randomised strategy trial using an allopurinol dosing model in Aotearoa/New Zealand (the Easy-Allo Study)
Authors: Stamp Lisa , Te Karu Leanne , Reid Susan , Wright Daniel F B , Frampton Chris , Tuitaupe Vui Suli , Dalbeth Nicola 
Published: August 2024

IntroductionGout is one of the most common forms of arthritis worldwide. Gout is particularly prevalent in Aotearoa/New Zealand and is estimated to affect 13.1% of Māori men, 22.9% of Pacific men and 7.4% of New Zealand European men. Effective long-term treatment requires lowering serum urate to <0.36 mmol/L. Allopurinol is the most commonly used urate-lowering medication worldwide. Despite its efficacy and safety, the allopurinol dose escalation treat-to-target serum urate strategy is difficult to implement and there are important inequities in allopurinol prescribing in Aotearoa. The escalation strategy is labour intensive, time consuming and costly for people with gout and the healthcare system. An easy and effective way to dose-escalate allopurinol is required, especially as gout disproportionately affects working-age Māori men and Pacific men, who frequently do not receive optimal care.Methods and analysis: A 12-month non-inferiority randomised controlled trial in people with gout who have a serum urate ≥ 0.36 mmol/l will be undertaken. 380 participants recruited from primary and secondary care will be randomised to one of the two allopurinol dosing strategies: intensive nurse-led treat-to-target serum urate dosing (intensive treat-to-target) or protocol-driven dose escalation based on dose predicted by an allopurinol dosing model (Easy-Allo). The primary endpoint will be the proportion of participants who achieve target serum urate (<0.36 mmol/L) at 12 months.Ethics and disseminationThe New Zealand Northern B Health and Disability Ethics Committee approved the study (2022 FULL 13478). Results will be disseminated in peer-reviewed journals and to participants.Trial registration numberACTRN12622001279718p.
Global burden of HIV among long-distance truck drivers: a systematic review and meta-analysis
Authors: Mutie Cyrus , Otieno Berrick , Mwangi Elijah , Kithuci Kawira , Mutisya Albanus , Gachohi John , Mbuthia Grace 
Published: August 2024

ObjectivesThe purpose of this study was to systematically summarise the empirical evidence on the prevalence of HIV among long-distance truck drivers (LDTDs) from all parts of the world.DesignA systematic review and meta-analysis were conducted.Data sourcesWe searched PubMed, ProQuest Central, PubMed Central, Cumulated Index to Nursing and Allied Health Literature and Global Index Medicus to identify relevant information published from 1989 to 16 May 2023.Eligibility criteriaPeer-reviewed publications of English language reporting on the prevalence of HIV among LDTDs were included. Non-empirical studies like literature reviews were excluded.Data extraction and synthesisUsing a standardised data abstraction form, we extracted information on study characteristics and HIV prevalence levels. Crude prevalence estimates per 100 participants were computed and later transformed using logit transformation to have them follow a normal distribution. A meta-analysis of prevalences using the random effects model was performed. The I2statistic was used to quantify the degree of heterogeneity across studies. A subgroup analysis using meta-regression was performed to investigate factors that could explain variability across studies. The Joanna Briggs Institute tools and Newcastle-Ottawa Scale were used to assess the quality of the included studies. To assess the certainty of evidence, the Grading of Recommendations Assessment, Development, and Evaluation approach was used.ResultsOf the 1787 articles identified, 42 were included. Most of the included studies were conducted in sub-Saharan Africa (45.23%, n=19) and Asia and the Pacific (35.71%, n=15). The pooled prevalence of HIV was 3.86%, 95% CI (2.22% to 6.64%). The burden of HIV was highest in sub-Saharan Africa at 14.34%, 95% CI (9.94% to 20.26%), followed by Asia and the Pacific at 2.12%, 95 CI (0.94% to 4.7%) and lastly Western, Central Europe and North America at 0.17%, 95% CI (0.03% to 0.82%). The overall heterogeneity score was (I2=98.2%, p<0.001).ConclusionThe global burden of HIV among LDTDs is 3.86%, six times higher than that of the general population globally. Compared with other regions, the burden of HIV is highest in sub-Saharan Africa at 14.34%, where it is estimated to be 3% in the general population. Thus, LDTDs endure a disproportionately high burden of HIV compared with other populations. Consequently, more LDTD-centred HIV research and surveillance is needed at national and regional levels to institute tailored preventive policies and interventions.PROSPERO registration numberCRD42023429390.