bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surveillance for
Chlamydia trachomatis
variants escaping detection with the Aptima Combo 2 assay in Canada from 2019 to 2021
Authors: Roy Felicia , Beirnes Jennifer , LeBlanc Jason J. , Gibbons Suzanne , Sivro Aida , Severini Alberto ,   On behalf of the Canadian Public Health Laboratory Network (CPHLN) Chlamydia Variant Working Group
Published: January 2025

ABSTRACT

Nucleic acid amplification tests (NAATs) are the method of choice for
Chlamydia trachomatis
diagnosis, but these strategies are susceptible to target site mutations.
C. trachomatis
variants escaping detection with the Aptima Combo 2 (AC2) assay on the Hologic Panther instrument from 23S rRNA mutations have been reported in Nordic countries, England, Japan, and the United States. Given the potential for false negative results, this study investigated whether strains of
C. trachomatis
with AC2 target site mutations were present in Canada. Surveillance was conducted in Canadian laboratories from 2019 to 2021. Specimens suspected of AC2 target site mutations included those with low-value detections on the AC2 assay, with subsequent high-value detections on the Aptima Chlamydia Trachomatis (ACT) assay used for confirmatory testing. Specimens with AC2/ACT discrepant results were subjected to sequencing of the AC2 target (i.e., 23S rRNA). Sequencing revealed 15 (4.8%) diagnostic escape variants which were carrying either C1514T, G1523A, or G1526A mutations. All specimens with
a
diagnostic escape mutation were detected with a reformulated version of the AC2 assay. Overall, while the prevalence of
C. trachomatis
variants was rare, their presence in the Canadian population supports the use of the new AC2 kit formulation and the need for ongoing genetic surveillance for NAAT-based assays.

IMPORTANCE

Molecular tests are commonly used for the detection of sexually transmitted infections (STIs) like
Chlamydia trachomatis
. Mutations impacting
C. trachomatis
molecular target detection on the Hologic Panther AC2 assay have been reported in several countries, raising concerns about potential false negative results. This study showed
C. trachomatis
target detection failures in specimens submitted for
C. trachomatis
testing in Canadian laboratories from 2019 to 2021. A reformulated version of the AC2 molecular test is now available that can identify
C. trachomatis
strains harboring target site mutations that were impacted by the previous test formulation. While target site mutations were rare in Canada, revealing their presence is important to ensure accurate molecular detection of
C. trachomatis
with existing testing methods. This study supports ongoing genetic monitoring of
C. trachomatis
molecular test target sites, as well as the use of the reformulated test to avoid false negative results and subsequent transmissions.
Variation and assembly mechanisms of
Rhinolophus ferrumequinum
skin and cave environmental fungal communities during hibernation periods
Authors: Leng Haixia , Li Aoqiang , Li Zhongle , Hoyt Joseph R. , Dai Wentao , Xiao Yanhong , Feng Jiang , Sun Keping 
Published: January 2025

ABSTRACT

Animal skin acts as the barrier against invasion by pathogens and microbial colonizers. Environmental microbiota plays a significant role in shaping these microbial communities, which, in turn, have profound implications for host health. Previous research has focused on characterizing microorganisms on bats’ skin and in their roosting environments, particularly bacterial communities. The emergence of white-nose syndrome, caused by the fungal-pathogen
Pseudogymnoascus destructans
, highlights the importance of understanding fungal dynamics in cave ecosystems and on bats’ skin. In this study, we employed ITS amplicon sequencing to investigate the fungal community associated with the skin of
Rhinolophus ferrumequinum
and surfaces within hibernacula. In addition, we utilized neutral community and null models to assess the relative importance of stochastic and deterministic processes in fungal community assembly. The infection status of
P. destructans
did not significantly impact fungal community composition either on bat skin or cave environments. However, fungal diversity was significantly higher in cave environments compared to bat skin. Notably, potentially inhibitory genera of fungal pathogens were present in both bats and cave environments during hibernation. Furthermore, the composition and structure of fungal communities on both bat skin and cave environments varied across hibernation periods. Our findings suggest neutral processes primarily drive the assembly of fungal communities associated with hibernating
R. ferrumequinum
and cave environments, with dispersal limitation exerting a significant influence. This study provides insights into the fungal communities associated with hibernating
R. ferrumequinum
and cave environments.

IMPORTANCE

Animal habitats provide sources and reservoirs for host microorganisms, making it critical to understand changes in microbial communities between habitats and hosts. While most studies have focused on bacterial microorganisms, research on fungal communities is lacking. This study investigated how community dynamics and assembly processes differ between the skin of hibernating
Rhinolophus ferrumequinum
and the cave environments under pathogen stress. We found significant differences in the composition and structure of the fungal communities between bat skin and roosting cave environments. Fungal genera with potential inhibitory effects on pathogens were found in all bat skin and cave environments. In addition, dispersal limitations during stochastic processes were a key factor in the formation of environmental fungal communities on bat skin and in caves. These findings offer new insights for exploring pathogen-host-environment-microbe interactions.
Fluid fluctuations assessed with artificial intelligence during the maintenance phase impact anti-vascular endothelial growth factor visual outcomes in a multicentre, routine clinical care national age-related macular degeneration database
Authors: Martin-Pinardel Ruben , Izquierdo-Serra Jordi , Bernal-Morales Carolina , De Zanet Sandro , Garay-Aramburu Gonzaga , Puzo Martin , Arruabarrena Carolina , Sararols Laura , Abraldes Maximino , Broc Laura , Escobar-Barranco Jose Juan , Figueroa Marta , Zapata Miguel Angel , Ruiz-Moreno José M , Parrado-Carrillo Alba , Moll-Udina Aina , Alforja Socorro , Figueras-Roca Marc , Gómez-Baldó Laia , Ciller Carlos , Apostolopoulos Stefanos , Mishchuk Anastasiia , Casaroli-Marano Ricardo P , Zarranz-Ventura Javier 
Published: January 2025

AimTo evaluate the impact of fluid volume fluctuations quantified with artificial intelligence in optical coherence tomography scans during the maintenance phase and visual outcomes at 12 and 24 months in a real-world, multicentre, national cohort of treatment-naïve neovascular age-related macular degeneration (nAMD) eyes.MethodsDemographics, visual acuity (VA) and number of injections were collected using the Fight Retinal Blindness tool. Intraretinal fluid (IRF), subretinal fluid (SRF), pigment epithelial detachment (PED), total fluid (TF) and central subfield thickness (CST) were quantified using the RetinAI Discovery tool. Fluctuations were defined as the SD of within-eye quantified values, and eyes were distributed according to SD quartiles for each biomarker.ResultsA total of 452 naïve nAMD eyes were included. Eyes with highest (Q4) versus lowest (Q1) fluid fluctuations showed significantly worse VA change (months 3–12) in IRF −3.91 versus 3.50 letters, PED −4.66 versus 3.29, TF −2.07 versus 2.97 and CST −1.85 versus 2.96 (all p<0.05), but not for SRF 0.66 versus 0.93 (p=0.91). Similar VA outcomes were observed at month 24 for PED −8.41 versus 4.98 (p<0.05), TF −7.38 versus 1.89 (p=0.07) and CST −10.58 versus 3.60 (p<0.05). The median number of injections (months 3–24) was significantly higher in Q4 versus Q1 eyes in IRF 9 versus 8, SRF 10 versus 8 and TF 10 versus 8 (all p<0.05).ConclusionThis multicentre study reports a negative effect in VA outcomes of fluid volume fluctuations during the maintenance phase in specific fluid compartments, suggesting that anatomical and functional treatment response patterns may be fluid-specific.
Triglyceride lowering in patients with different severities of hypertriglyceridaemia-associated acute pancreatitis: secondary analysis of a multicentre, prospective cohort study
Authors: Luo Xiang , Li Xiaoling , Lai Xiaoyan , Mao Wenjian , Ke Lu , Fu Lingyan , Gao Lin , Liu Yaolu 
Published: January 2025

ObjectiveIt is controversial whether rapid lowering of triglyceride (TG) levels is associated with clinical benefits in patients with hypertriglyceridaemia-associated acute pancreatitis (HTG-AP). In particular, patients with different severity of disease may respond differently to TG-lowering therapy. In this study, we aimed to explore the association between rapid decline in serum TG levels and organ failure in patients with different severities of HTG-AP.MethodsThis is a secondary analysis of data from a multicentre, prospective registry recruiting HTG-AP patients admitted within 72 hours from the onset of symptoms. Patients were dichotomised into either target reaching (TG≤5.65 mmol/L on study day 3) or not. The primary outcome was the presence of organ failure at day 14. The association between target-reaching and the primary outcome was modelled. Furthermore, subgroup analyses were conducted based on the disease severity of HTG-AP patients at enrolment.ResultsOverall, 413 patients were included for analysis, of whom 192 (46.5%) reached the target on day 3. For the overall study cohort, there was no significant difference in presence of organ failure at day 14 between patients reaching the target or not (3.1% vs 6.8%, p=0.091). In the subgroup of HTG-AP patients with organ failure at enrolment, compared with patients with TG>5.65 mmol/L on day 3, patients who reached the target had significantly lower presence of organ failure at day 14 (7.8% vs 22%, p=0.039) and lower incidence of infected pancreatic necrosis within 60 days (3.1% vs 11.9%, p=0.049). Similar findings were seen in the subgroup with more severe HTG-AP (APACHE II ≥8 at enrolment).ConclusionMore rapid decline of serum TG levels was associated with decreased presence of organ failure at day 14 in patients with more severe HTG-AP.Trial registration numberThe Chinese Clinical Trial Registry, number ChiCTR2000039541.
Cervical cancer screening by cotesting method for Vietnamese women 25–55 years old: a cost-effectiveness analysis
Authors: Bui Hien Thu , Pham Van Nu Hanh , Vu Thang Hong 
Published: January 2025

BackgroundCervical cancer (CC) is preventable through regular screening and vaccination against human papillomavirus (HPV). However, CC remains a significant public health issue in low-income and middle-income countries (LMICs) like Vietnam, where financial constraints hinder the widespread implementation of HPV vaccination and screening programmes. Currently, Vietnam lacks both a national CC screening intervention and an HPV vaccination programme for women and girls. To date, cost-effectiveness studies evaluating CC screening methods in Vietnam remain limited.ObjectivesTo evaluate the cost-effectiveness of two CC screening strategies for Vietnamese women aged 25–55 years: (1) cotesting combining cytology and HPV testing conducted three times at 5 year intervals (intervention) and (2) cytology-based screening conducted five times at 2 year intervals (comparator). The objective is to provide evidence to inform policy and clinical practice in Vietnam.DesignCost-effectiveness analysis using a Markov model with 1 year cycles to simulate the natural progression of CC.SettingThe Vietnamese healthcare system, modelled from the provider’s perspective, with parameters adapted to the local context through expert consultations.ParticipantsA simulated cohort of Vietnamese women aged 25–55 years.InterventionsThe intervention involved cotesting (cytology and HPV testing) three times at 5 year intervals. The comparator was cytology-based screening conducted five times at 2 year intervals.Primary and secondary outcome measuresThe primary outcome measure was quality-adjusted life years (QALYs). Costs and cost-effectiveness ratios were assessed using Vietnam’s gross domestic product (GDP) per capita as the cost-effectiveness threshold (1–3 times GDP per capita). Sensitivity analyses (one-way deterministic and probabilistic) were conducted to account for uncertainties.ResultsThe cotesting strategy was less effective and more costly than cytology-based screening across all age groups. Cotesting resulted in higher costs and fewer QALYs than the comparator. Probabilistic sensitivity analyses confirmed that cotesting was not cost-effective under current conditions in Vietnam.ConclusionsCytology-based screening conducted five times at 2 year intervals is a more cost-effective option for CC screening in Vietnamese women aged 25–55 years. The cotesting strategy cannot be recommended due to its higher cost and lower effectiveness.
Effect of propofol and ciprofol in patients undergoing bronchoscopy: protocol for a double-blind, randomised controlled trial
Authors: Tang Jinxuan , Chen Fang , Huang Jiayu , Li Dongliang , Li Cheng 
Published: January 2025

IntroductionPropofol is a fast-acting intravenous anaesthetic widely used for sedation and anaesthesia in gastrointestinal endoscopy, bronchoscopy, and the induction/maintenance of general anaesthesia in outpatients and inpatients; however, propofol has several undesirable effects, including injection pain, which affects the physical and mental health of patients, and cardiopulmonary depression, characterised by hypotension, bradycardia and apnea, which commonly occur in clinical practice. Ciprofol (HSK3486) is a propofol analogue with good clinical safety, high potency and some advantages over propofol, including lower injection pain and haemodynamic depression in patients undergoing gastroscopy and colonoscopy. This study aims to compare the impact of equivalent effective doses of propofol and ciprofol on haemodynamic changes in patients undergoing bronchoscopy under general anaesthesia.MethodsThis prospective, double-blind, randomised, controlled clinical trial will recruit 250 patients aged 18–80 years scheduled for elective bronchoscopy under general anaesthesia. The cohort will be randomised into two groups in a 1:1 ratio: propofol (200 mg/20 mL of saline) and ciprofol (40 mg/20 mL of saline). The primary outcomes are changes in heart rate and blood pressure before and after induction, laryngeal mask airway (LMA) placement and bronchoscopy placement. The secondary outcomes are the incidence of choking and injection pain, the type and dose of vasoactive drugs used during the operation, and the level of postoperative satisfaction among surgeons, anaesthesiologists and patients.Ethics and disseminationThis trial was approved by the Medical Ethics Committee of Shanghai Fourth People’s Hospital, School of Medicine, Tongji University and registered with the Chinese Clinical Trials Registry (Identifier: ChiCTR2200063048) on 29 August 2022. The findings of this study will be disseminated through various channels. Academic dissemination will include publication in peer-reviewed journals and presentations at national and international conferences.Trial registration numberChiCTR2200063048.
Diagnostic performance of the DISQVER metagenomic sequencing tool for the identification of pathogens in febrile neutropenic patients: the ADNEMIA trial
Authors: Pichon Maxime , Burucoa Christophe 
Published: January 2025

IntroductionWhile intensive protocols in onco-haematology have improved survival rates for patients with haematological malignancies, they have also resulted in an increased incidence of infection associated with therapy-induced immunosuppression (including chemotherapy-induced febrile neutropenia; FN). The occurrence of FN, associated with high morbidity and mortality, necessitates broad-spectrum antibiotic therapy, occasioning delayed chemotherapy and resulting in a loss of opportunity for the patient. Considering that without an identified pathogen, a 10% mortality rate can ensue, documentation is essential to the optimisation of antibiotic therapy. However, blood culture (the reference test) is limited for several reasons: such as fastidious culture, antibiotic treatment prior to sampling or insufficient sample volume. Sequencing technologies have led to the development of diagnostic approaches based on the detection of circulating DNA in blood. This study will aim to assess the clinical utility of metagenomic next-generation sequencing (mNGS)-DISQVER technology in detecting pathogenic microorganisms from blood samples of patients undergoing high-risk FN treatment.Methods and analysisThis nationwide, prospective, multicentre, interventional, proof-of-concept clinical trial will enrol 200 patients. Will include patients≥18 years old, treated for malignancy, at high risk of FN (Multinational Association for Supportive Care in Cancer score≤21) with an expected duration of neutropenia≥7 days. Patients who received antibiotic treatment within 24 hours prior to enrolment, have previously participated and/or have enhanced protection will be excluded. The primary outcome will be determined by considering the microorganisms responsible for this FN, weighted by the assessment of an adjudication committee. Secondary outcomes will evaluate patient management depending on the arm. The second secondary outcome will be determined by the duration of conventional assessment, frequency of microorganisms detected during routine care and percentage distribution of theoretical adjustments made to anti-infective treatment based on microorganisms diagnosed using the mNGS-DISQVER tool as compared with conventional practices. Identifying the pathogens responsible for high-risk FN from a blood sample, using an unbiased technique, can provide microbiological documentation and may even reveal unexpected microorganisms in these profoundly immunocompromised patients.Ethics and disseminationThe protocol received approval from the Comité de Protection des Personnes Sud-Méditerranée II. All participants will provide informed consent before participation. The trial has been registered on ClinicalTrials.gov (identifierNCT06075888). The results of the main trial and each of the secondary endpoints will be submitted for publication in a peer-reviewed journal.Trial registration numberClinicalTrials.govNCT06075888.
Adapting a consensus process for survivors of domestic abuse and child maltreatment: a brief report about adopting a trauma-informed approach in multistakeholder workshops
Authors: Powell Claire , Szilassy Eszter , Cowan Katherine , Feder Gene , Gilbert Ruth , Howarth Emma , Johns Karen , Lindenberg Ursula , Gregory Alison 
Published: January 2025

PurposeAmong health researchers, there is a growing appreciation of the importance of the involvement of service users and members of the public. This recognition has not only resulted in involvement guidelines and improved research ethics but also an increasing use of consensus processes with service users and members of the public to determine research priorities and questions and to agree outcomes to be measured in intervention studies. There is, however, limited advice about how to safely involve survivors of violence and abuse in consensus-based studies.Methods/resultsThis commentary provides an overview of the adaptations made to a process of core outcome set development, to ensure that survivors of violence and abuse felt safe, heard and supported, and able to contribute in a meaningful way.ConclusionsWe advocate for an iterative process of listening to and learning from survivors, as well as buy-in from funders to ensure research studies are appropriately resourced and involve sufficient planning time.
Impact of primary care benefits on healthcare utilisation and estimated out-of-pocket expenses in urban, rural and remote settings in the Philippines
Authors: Panganiban Janelle Micaela S , Camiling-Alfonso Romelei , Sanchez Josephine T , De Mesa Regine Ynez H , Sandigan Gillian , Amit Arianna Maever L , Rey Mia P , Lopez Johanna Faye E , Fabian Noleen Marie , Galingana Cara Lois T , Bernal-Sundiang Nannette , Aquino Maria Rhodora N , Lastrilla Chad Lester , Callo Miguel , Tan-Lim Carol Stephanie Chua , Dans Leonila F , Marfori Jose Rafael A , Paterno Ramon Pedro , Dans Antonio L 
Published: January 2025

BackgroundThis study aimed to determine the effects of primary care interventions on healthcare utilisation and estimated out-of-pocket (OOP) expenses in selected urban, rural and remote settings in the Philippines.MethodologyContext-specific measures relating to expanding healthcare provider networks, augmenting the health human workforce and subsidising transportation costs were implemented to strengthen primary care systems. In this study, two key outcomes were monitored: (1) monthly healthcare utilisation measured by the total number of outpatient consultations per site and (2) change in OOP expenses from baseline to endline within a 1 year study period.ResultsAll sites had a positive trend in monthly outpatient consultations in healthcare utilisation over 1 year. The remote site had the steepest increase in outpatient consultations, with a 401% increase compared with the baseline during the peak of consultations at month 7. The urban site had a 62% increase in outpatient consultations from baseline to month 6, while the rural site had a 251% increase from baseline to month 11, which corresponded to the peak month in terms of the number of outpatient consultations. The rural site had the largest decrease in estimated OOP expenses (50.3% reduction, 95% CI −88 to –13), followed by the remote site (33.2% reduction, 95% CI −67,+1) and the urban site (16.0% reduction, 95% CI −65,+33).ConclusionThe rural site showed a significant reduction in estimated OOP expenses and an increase in healthcare utilisation. The remote site had the steepest increase in utilisation, but the reduction in estimated OOP expenses was not statistically significant. The urban site experienced the lowest increase in utilisation, and the smallest reduction in estimated OOP expenses, which was also not statistically significant. Implementing primary care benefits will necessitate contextualised approaches to avoid the inadvertent aggravation of inequities in healthcare.