bluuebunny/crossref_metadata_2025_split huggingface dataset:
First-year dynamics of the anaerobic microbiome and archaeome in infants’ oral and gastrointestinal systems
Authors: Neumann Charlotte J. , Mohammadzadeh Rokhsareh , Woh Pei Yee , Kobal Tanja , Pausan Manuela-Raluca , Shinde Tejus , Haid Victoria , Mertelj Polona , Weiss Eva-Christine , Kolovetsiou-Kreiner Vassiliki , Mahnert Alexander , Kumpitsch Christina , Jantscher-Krenn Evelyn , Moissl-Eichinger Christine 
Published: December 2024

ABSTRACT

Recent research provides new insights into the early establishment of the infant gut microbiome, emphasizing the influence of breastfeeding on the development of gastrointestinal microbiomes. In our study, we longitudinally examined the taxonomic and functional dynamics of the oral and gastrointestinal tract (GIT) microbiomes of healthy infants (
n
= 30) in their first year, focusing on the often-over-looked aspects, the development of archaeal and anaerobic microbiomes. Breastfed (BF) infants exhibit a more defined transitional phase in their oral microbiome compared to non-breastfed (NBF) infants, marked by a decrease in
Streptococcus
and the emergence of anaerobic genera such as
Granulicatella
. This phase, characterized by increased alpha-diversity and significant changes in beta-diversity, occurs earlier in NBF infants (months 1–3) than in BF infants (months 4–6), suggesting that breastfeeding supports later, more defined microbiome maturation. We demonstrated the presence of archaea in the infant oral cavity and GIT microbiome from early infancy, with
Methanobrevibacter
being the predominant genus. Still, transient patterns show that no stable archaeome is formed. The GIT microbiome exhibited gradual development, with BF infants showing increased diversity and complexity between the third and eighth months, marked by anaerobic microbial networks. NBF infants showed complex microbial co-occurrence patterns from the start. These strong differences between BF and NBF infants’ GIT microbiomes are less pronounced on functional levels than on taxonomic levels. Overall, the infant microbiome differentiates and stabilizes over the first year, with breastfeeding playing a crucial role in shaping anaerobic microbial networks and overall microbiome maturation.

IMPORTANCE
The first year of life is a crucial period for establishing a healthy human microbiome. Our study analyses the role of archaea and obligate anaerobes in the development of the human oral and gut microbiome, with a specific focus on the impact of breastfeeding in this process. Our findings demonstrated that the oral and gut microbiomes of breastfed infants undergo distinct phases of increased dynamics within the first year of life. In contrast, the microbiomes of non-breastfed infants are more mature from the first month, leading to a steadier development without distinct transitional phases in the first year. Additionally, we found that archaeal signatures are present in infants under 1 year of age, but they do not form a stable archaeome. In contrast to this, we could track specific bacterial strains transitioning from oral to gut or persisting in the gut over time.
Exploiting gasdermin-mediated pyroptosis for enhanced antimicrobial activity of phage endolysin against
Pseudomonas aeruginosa
Authors: Kuc-Ciepluch Dorota , Ciepluch Karol , Augustyniak Daria , Guła Grzegorz , Maciejewska Barbara , Kowalik Artur , Jop Ewelina , Drulis-Kawa Zuzanna , Arabski Michał 
Published: December 2024

ABSTRACT

Pyroptosis is an inflammatory immune response of eukaryotic cells to bacterial lipopolysaccharide (LPS) and other pathological stimuli, leading to the activation of the gasdermin D (GSDMD) and secretion of pore-forming domain GSDMD
Nterm
, facilitating the release of cytokines. Additionally, GSDMD
Nterm
exhibits antibacterial properties through interactions with bacterial outer membranes (OM). We explored alternative antimicrobial strategy to determine whether inducing natural pyroptosis via GSDMD activation by
P. aeruginosa
LPS could enhance the effectiveness of recombinant phage endopeptidase KP27 (peptidoglycan-degrading enzyme) against
P. aeruginosa
, enabling penetration through OM and bacterial killing synergistically. Our findings demonstrated that recombinant GSDMD alone exhibited antibacterial effects against wild-type
P. aeruginosa
with smooth LPS, while recombinant GSDMD
Nterm
efficiently permeabilized both smooth LPS-bearing and O-chain-deficient
P. aeruginosa
potentially synergizing with endolysin KP27. Transcriptomic analyses revealed the activation of the immune system pathways in response to LPS, mainly in monocytic cells, in contrast to epithelial A549 or HeLa cell lines. LPS-induced pyroptosis in monocytes led to GSDMD cleavage and the release of interleukins, regardless of the nature/origin of the LPS used. However, the pyroptosis stimulation by LPS in the antibacterial assay was not effective enough for bacterial OM permeabilization and enhancement of endolysin activity. We assume that leveraging pyroptosis induction in monocytic cells to augment the bactericidal activity of endolysins may be limited.

IMPORTANCE

Recombinant GSDMD
Nterm
protein was able to efficiently permeabilize
P. aeruginosa
outer membranes and increase endolysin activity against bacteria, producing either long LPS O-chains or lack them entirely. The obtained results suggest the limited possibility of using the natural process of pyroptosis occurring in monocytic cells to enhance the bactericidal effect of recombinant phage endolysins against Gram-negative bacteria infection.
Another way? An investigation into an institution’s use of the Wayson stain in re-evaluating “no organisms seen” on Gram stain smears from positive blood cultures
Authors: Attaway Christopher C. , Smith Jessica , Rhoads Daniel D. 
Published: December 2024

ABSTRACT

Automated continuous monitoring blood culture instruments identify metabolism byproducts and flag blood culture bottles as “positive.” A Gram stain is used to visualize and characterize the microbial growth in the broth and initiate additional testing. When no organisms are seen (NOS) on Gram stain, in our laboratory, bottles are reevaluated with a Wayson stain, a rapid one-step stain that provides contrast between organisms and the background, especially in Gram-negative organisms. In this study, we assess the performance of the Wayson stain on reevaluation of Gram stain NOS blood culture bottles. The study period, August 2022 to July 2023, includes blood cultures that were flagged as positive by the automated blood culture instrument (BACTEC) with accompanying Gram and Wayson stain interpretations and organism identification. 133,463 blood cultures were performed during the study period, and 20,129 cultures were flagged as positive by BACTEC. 601 NOS Gram stain cultures were identified of which 76 had a positive Wayson. The Wayson stain procedure increased the sensitivity of direct organism visualization from 99.32% to 99.71% by identifying 55% (76 of 137) of NOS Gram stain blood culture bottles. Of blood cultures that were positive by BACTEC with NOS Gram and Wayson stains (475), 414 were finalized as no growth and 61 had an isolate (false negatives) of which 49% (30) were yeasts. The Wayson stain aided in detecting gram-negative genera such as
Capnocytophaga
,
Campylobacter
, and
Fusobacterium
species and other rarely identified species.

IMPORTANCE

The Wayson stain, a rapid one-step stain that provides contrast between microorganisms and the background, was historically used for the presumptive diagnosis of
Yersinia pestis
from bubo specimen. In our laboratory, the Wayson stain has long been used to reevaluate blood culture Gram-stained smears from bottles that were flagged as positive by the automated continuous monitoring instrument but where no organisms are seen. In this study, we show that the Wayson stain provides an easily implemented and interpreted technique, other than a repeat Gram stain or acridine orange, to increase the sensitivity of direct organism visualization from blood culture bottles, particularly for Gram-negative organisms.
Cohort profile: the potentially preventable burden of community-acquired pneumonia in South African adults in the era of widespread PCV13 immunisation and antiretroviral therapy roll-out, before and during the COVID-19 pandemic – the multicentre, multimethod PotPrev Study
Authors: Nabeemeeah Firdaus , Sabet Nadia , Otwombe Kennedy , Hlongwane Khuthadzo , Mlambo Lebohang M , Moloantoa Tumelo , Wong Michelle , Mangena Phetho , Abraham Pattamukkil , Swanepoel Floris , Moosa Fahima , von Gottberg Anne , Cohen Cheryl , Southern Jo , Fletcher Mark , Dunne Eileen , Ndungane-Tlakula Bha , Begier Elizabeth , Gray Sharon , Gessner Bradford D , Naidoo Jerusha , Milovanovic Minja , Variava Ebrahim , Martinson Neil 
Published: December 2024

PurposeIn the setting of an established childhood pneumococcal vaccination programme with immediate initiation and treatment of antiretroviral therapy (ART) for people living with HIV (PLWH), the risk of adult pneumococcal community-acquired pneumonia (CAP) is not recently described. We aimed to investigate CAP incidence, recurrence, mortality, risk factors and microbiology before and during the COVID-19 pandemic.ParticipantsAdults aged ≥18 years were enrolled in three South African provinces from March 2019 to October 2021, with a brief halt during the initial COVID-19 lockdown. The first group, PdCAP, a surveillance cohort, had their data abstracted to estimate the population incidence of physician-diagnosed CAP by counting incident CAP patients presenting to emergency rooms (ER) and mapping them to catchment areas linked to census data. From those admitted to wards from ERs, a prospective cohort (HospCAP) was enrolled and followed up to 1 year after discharge. Microbiology testing was performed and data were abstracted and collected for economic assessments. A third group (StART) of PLWH without respiratory illness at enrolment, attending primary healthcare clinics to initiate or reinitiate ART, was prospectively enrolled and followed. HospCAP and StART participants (totalling 2950 participants) were followed for at least 1 year and assessed for CAP episodes, hospitalisations and mortality.Findings to dateSurveillance identified 6546 patients attending ERs with physician-diagnosed CAP; 61/6546 (0.9%) died in the ER. We prospectively enrolled 2000 hospitalised patients with CAP of whom 1079/2000 (54.0%) were PLWH. Overall, 271/2000 (13.6%) hospitalised CAP patients died during their first admission and 298/2000 (14.9%) died during follow-up. Among StART cohort, 18/950 (1.9%) died during follow-up.Future plansPlanned analyses include incidence estimates of pneumococcal serotype-specific adult CAP and its recurrence, using Urinary Antigen Detection assay results to model the burden of pneumococcal CAP better and health economics analyses.
Efficacy of solution-focused brief therapy versus case management for psychological distress in adolescents and young adults in a community-based youth mental health service in Singapore: protocol for a randomised controlled trial
Authors: Foo Cheryl Yunn Shee , Hui Tianyi , Ngaiman Nur Khairunisa Binte , Dahjalarrajah Darshan s/o , Chua Yi Chian , Lee Yi Ping , Abdin Edimansyah , Vaingankar Janhavi Ajit , Tang Charmaine 
Published: December 2024

IntroductionThere are insufficient scalable, evidence-based treatments to meet increasing mental health needs of young people. Offering interim, brief interventions for young persons with psychological distress can improve access to care and mitigate adverse effects of long waiting times. This study tests the efficacy of solution-focused brief therapy (SFBT), a strength-based, goal-directed intervention, in adolescents and young adults at a community-based youth mental health service in Singapore.Methods and analysisThis is a fully powered, randomised, single-centre, two-arm, parallel, superiority, controlled trial. From September 2023 to March 2025, the study will recruit 124 participants (aged 16–30) presenting at a national youth mental health service in Singapore (CHAT, Centre of Excellence for Youth Mental Health) with clinically assessed general psychological distress, subthreshold or prodromal symptoms, or a first episode of a mood disorder. Participants will be excluded if they have high risk of suicide, psychosis, cognitive impairments, or current psychological treatments. Participants will be randomised in a 1:1 ratio to receive six-session, case manager delivered SFBT or treatment as usual (TAU) case management, and be followed up for 3 months post-intervention. Participants receiving SFBT are hypothesised to have greater improvements in self-reported psychological distress, from baseline to 8 weeks, compared with the control group. Secondary outcomes are self-reported depression and anxiety symptoms, and functional impairment. The study will also explore whether SFBT is associated with increased self-efficacy and decreased hopelessness, decreased downstream referrals post-intervention, and sustained clinical gains 3 months post-intervention compared with TAU. Adverse events and clinical deterioration will be recorded and reported.Ethics and disseminationThe Institute of Mental Health (IMH) Institutional Research Review Committee (reference 822–2022) and the Singapore National Health Group Domain Specific Review Board (DSRB) (reference 2023/00052) have approved the study protocol. Findings will be published in international, peer-reviewed scientific journals. Summaries will be disseminated to study funders, mental healthcare systems administrators, and clinicians.Trial registration numberISRCTN13671612https://doi.org/10.1186/ISRCTN13671612
Long-term sickness absence trajectories and associated occupational and lifestyle-related factors: a longitudinal study among young and early midlife Finnish employees with pain
Authors: Fagerlund Pi , Shiri Rahman , Walker-Bone Karen , Rahkonen Ossi , Lallukka Tea 
Published: December 2024

ObjectivesThis study aimed to identify distinct trajectories of long-term sickness absence (LTSA, >10 consecutive working days) among young and early midlife Finnish employees who experienced pain at baseline. It also aimed to determine the pain characteristics and occupational and lifestyle factors associated with these LTSA patterns.DesignLongitudinal occupational cohort study with register linkage.SettingThe largest municipal employer in Finland.ParticipantsThe study population comprised 19–39-year-old Finnish municipal employees (n=1685) who reported pain in 2017.Outcome measuresProspective register data on all-cause LTSA through March 2020 were obtained from the Social Insurance Institution of Finland. Group-based trajectory modelling was used to identify distinct all-cause LTSA trajectories. Multinomial logistic regression was used to examine associations of pain characteristics and work- and lifestyle-related factors with trajectory group membership.ResultsThree distinct LTSA-trajectory groups were identified: no LTSA (74%), decreasing (18%) and increasing (8%). The decreasing trajectory group had a higher prevalence of chronic or multisite pain, smoking (average marginal effects (AME) 6% points, 95% CI 2 to 11), obesity (AME 8% points, 95% CI 2 to 13), manual or routine non-manual occupation (AME 9% points, 95% CI 4 to 13) and high physical workload, after adjusting for age and gender. No predictor was identified for the increasing trajectory.ConclusionA majority of young and early midlife employees with pain had no LTSA during follow-up; however, chronic and multisite pain, smoking, overweight or obesity, lower occupational class and higher physical workload were associated with the decreasing LTSA trajectory. Interventions at workplaces and in occupational healthcare to prevent LTSA should aim at supporting employees who work with pain and have these risk factors.
Physician’s perception and practices on antimicrobial resistance in a tertiary care hospital in Bangladesh: a cross-sectional study
Authors: Haque Mohibbul , Karim Mohammad Rezaul , Shohid Sabrin , Choudhury Shadman Sakib , Hossain Pilot , Sen Rotna Rani , Dey Chaity , Khan Sumaiya , Munni Meherun Nahar , Shopna Sonia Afroze , Shultana Razia , Al Fidah Md Fuad , Khan Md Abdullah Saeed , Farhana Nasreen 
Published: December 2024

BackgroundAntimicrobial resistance (AMR) is a global health and development concern. Antimicrobial misuse and overuse are key contributors to the emergence of drug-resistant infections.ObjectiveThe current study aimed to determine the level of perception and practices of physicians regarding AMR in a tertiary-level hospital.DesignCross-sectional study.SettingA tertiary care hospital in Dhaka, Bangladesh.ParticipantsThe study included 360 physicians who worked for more than 6 months in different departments of the hospital.Primary and secondary outcome measuresPerceptions of AMR among physicians and secondary outcome measures were to find out the practices of physicians regarding AMR. The current study used 8 defined responses and 6 multiple-choice questions for scoring physicians’ perception of AMR and 12 items to score physicians’ self-reported practice regarding AMR. After converting these scores into percentages, the median split method was used to categorise them into poor and good categories.ResultsAmong 360 physicians, 51% were male, the median (IQR) age was 30 (27.0–34.0) years and 46% had private practices. More than half (52%) had a poor perception of AMR but had good practice (57%) with no significant association between perception and practice. The perception of AMR was significantly associated with age (p=0.048), years in practice (p=0.011) and AMR training (p=0.030). Physicians with private practice had 1.71 times higher odds of having a good perception of AMR (95% CI 2.07 to 2.75, p=0.026) and 2.44 times higher odds of having good practice (95% CI 1.51 to 3.94, p<0.001). The odds of having a good perception of AMR increase 1.20 times with a 1-year increase in years of practice (95% CI 1.01 to 1.44, p=0.042).ConclusionThe study revealed that most physicians had poor perception but good practice regarding AMR. Both poor perception and good practice were associated with private practice. To increase good practice and perception regarding AMR, efforts need to be made to establish an AMR education programme for practicing physicians as soon as possible. Moreover, medical audits and continuous quality improvement (such as programmes for antimicrobial stewardship) should be legislated, and monitoring prescribing behaviour and formulating policies accordingly are the way forward in combating AMR.
Healthcare ethics and artificial intelligence: a UK doctor survey
Authors: Warrington Daniel Joseph , Holm Søren 
Published: December 2024

ObjectivesTo survey UK doctors on their uses of artificial intelligence (AI) and of their views on the ethics and regulation of AI in healthcare.DesignAnonymous cross-sectional e-survey.SettingAn online survey of UK General Medical Council (GMC) registered doctors.Participants272 individuals.Main outcome measuresLikert-scale responses to questions covering personal use of AI, concerns about AI, requirements for introduction of AI and views on necessary AI regulation in healthcare.ResultsMost doctors rated themselves as slightly or moderately knowledgeable about AI, with men rating their knowledge levels higher than women. Doctors in training are more likely to have used AI than doctors after training. 37% of doctors who use AI reported using AI to help write the required reflective pieces for their portfolio. Doctors reported concerns about AI regarding patient safety and patients' right to confidentiality. They also expressed a strong desire for further regulation of AI in healthcare and, specifically, for their professional bodies to draft guidelines for the use of AI by doctors.ConclusionsThis study provides useful insights into UK doctors’ uses of AI in healthcare and their opinions on its introduction and regulation. It provides a case for guidance on the use of AI in the reflective practices of doctors and for further evaluation of doctors’ concerns about AI in healthcare. We call on doctors’ professional bodies (GMC, BMA and royal colleges) to draft professional guidance for doctors using AI.
Impact of alternative diagnostic labels for melanoma in situ on management choices and psychological outcomes: protocol for an online randomised study
Authors: Wu Zhuohan , Nickel Brooke , Boroumand Farzaneh , Elder David , Ferguson Peter M , Scolyer Richard A , O'Brien Blake , Barnhill Raymond , Adamson Adewole S , van Akkooi Alexander C J , Emery Jon , Parker Lisa , Low Donald , Low Cynthia , Davies Elspeth , Liu Sherrie , Lewis Stacey , Spongberg-Ross Bella , Bell Katy JL 
Published: December 2024

IntroductionA diagnosis of melanoma in situ presents negligible risk to a person’s lifespan or physical well-being, but existing terminology makes it difficult for patients to distinguish these from higher risk invasive melanomas. This study aims to explore whether using an alternative label for melanoma in situ may influence patients’ management choices and anxiety levels.Methods and analysisThis study is a between-subjects randomised online experiment, using hypothetical scenarios. Following consent, eligible participants will be randomised 1:1:1 to three labels: ‘melanoma in situ’ (control), ‘low-risk melanocytic neoplasm’ (intervention 1) and ‘low-risk melanocytic neoplasm, in situ’ (intervention 2). The required sample size is 1668 people. The co-primary outcomes are (1) choice between no further surgery or further surgery to ensure clear histological margins greater than 5 mm and (2) choice between patient-initiated clinical follow-up when needed (patient-led surveillance) and regular routinely scheduled clinical follow-up (clinician-led surveillance). Secondary outcomes include diagnosis anxiety, perceived risk of invasive melanoma and of dying from melanoma and management choice anxiety (after surgery choice and follow-up choice). We will make pairwise comparisons across the three diagnostic label groups using regression models (univariable and multivariable).Ethics and disseminationThe study has been registered with the Australian New Zealand Clinical Trials Registry (ACTRN12624000740594). Ethics approval has been received from The University of Sydney Human Research Ethics Committee (2024/HE000019). The results of the study will be published in a peer-reviewed medical journal, and a plain language summary of the findings will be shared on the Wiser Healthcare publication page (https://www.wiserhealthcare.org.au/category/publications/).Trial registration numberAustralian New Zealand Clinical Trials Registry (ID 386943).