bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neural network-based predictions of antimicrobial resistance phenotypes in multidrug-resistant
Acinetobacter baumannii
from whole genome sequencing and gene expression
Authors: Jia Huiqiong , Li Xinyang , Zhuang Yilu , Wu Yuye , Shi Shasha , Sun Qingyang , He Fang , Liang Shanyan , Wang Jianfeng , Draz Mohamed S. , Xie Xinyou , Zhang Jun , Yang Qing , Ruan Zhi 
Published: November 2024

ABSTRACT

Whole genome sequencing (WGS) potentially represents a rapid approach for antimicrobial resistance genotype-to-phenotype prediction. However, the challenge still exists to predict fully minimum inhibitory concentrations (MICs) and antimicrobial susceptibility phenotypes based on WGS data. This study aimed to establish an artificial intelligence-based computational approach in predicting antimicrobial susceptibilities of multidrug-resistant
Acinetobacter baumannii
from WGS and gene expression data. Antimicrobial susceptibility testing (AST) was performed using the broth microdilution method for 10 antimicrobial agents.
In silico
multilocus sequence typing (MLST), antimicrobial resistance genes, and phylogeny based on cgSNP and cgMLST strategies were analyzed. High-throughput qPCR was performed to measure the expression level of antimicrobial resistance (AMR) genes. Most isolates exhibited a high level of resistance to most of the tested antimicrobial agents, with the majority belonging to the IC2/CC92 lineage. Phylogenetic analysis revealed undetected transmission events or local outbreaks. The percentage agreements between AMR phenotype and genotype ranged from 70.08% to 89.96%, with the coefficient of agreement (κ) extending from 0.025 and 0.881. The prediction of AST employed by deep neural network models achieved an accuracy of up to 98.64% on the testing data set. Additionally, several linear regression models demonstrated high prediction accuracy, reaching up to 86.15% within an error range of one gradient, indicating a linear relationship between certain gene expressions and the corresponding antimicrobial MICs. In conclusion, neural network-based predictions could be used as a tool for the surveillance of antimicrobial resistance in multidrug-resistant
A. baumannii
.
Complete genome sequence of a nitrogen-fixing bacterium,
Klebsiella pasteurii
(formerly
Klebsiella oxytoca
) NG13, a rice rhizosphere isolate
Authors: Yoshidome Daisuke , Hidaka Makoto , Kosono Saori , Nishiyama Makoto 
Published: November 2024

ABSTRACT

Klebsiella oxytoca
NG13 was isolated from the rice rhizosphere in the early 1980s, and its nitrogen-fixing ability has been investigated. For the further advanced research, we sequenced its genome. NG13 contains one chromosome of 5,897,538 bp and no plasmid. NG13 should be classified to
Klebsiella pasteurii
based on ANI.
Antibiotic resistance and serotype distribution of
Shigella
strains in Bangladesh over the period of 2014–2022: evidence from a nationwide hospital-based surveillance for cholera and other diarrheal diseases
Authors: Afrad Mokibul Hassan , Islam Md. Taufiqul , Begum Yasmin Ara , Saifullah Md. , Ahmmed Faisal , Khan Zahid Hasan , Habib Zakir Hossain , Alam Ahmed Nawsher , Shirin Tahmina , Bhuiyan Taufiqur Rahman , Ryan Edward T. , Khan Ashraful Islam , Qadri Firdausi 
Published: November 2024

ABSTRACT

The objective of this study was to assess the prevalence, antimicrobial resistance patterns, and risk factors linked to
Shigella
infections through a nationwide hospital-based diarrheal disease surveillance in Bangladesh. From May 2014 to May 2022, from a systematic sentinel surveillance of
Shigella
infections in over 10 hospitals across Bangladesh, stool specimens were collected from patients with acute watery diarrhea and tested for
Shigella
species by microbiological culture. The susceptibility to antibiotics was tested using the disk diffusion method. Structured questionnaires were used to collect participants’ socioeconomic status and clinical, sanitation, and food history. Out of 24,357 stool specimens, 1.8% were positive for
Shigella
species, with a higher prevalence among males (58%). Children in the 6–17 age group were found to be at the highest risk of
Shigella
infections. The most prevalent serotype was
Shigella flexneri
(79.5%), followed by
Shigella sonnei. S. flexneri
serotype 2a was the most common (63.3%) among all
Shigella
serotypes. Antibiotic susceptibility testing showed over 99% of isolates resistant or with intermediate susceptibility to one of the seven antibiotics tested. About 96% of
S. flexneri
and all
S. sonnei
isolates demonstrated resistance to at least one quinolone class of antibiotics, particularly ciprofloxacin or nalidixic acid.
S. sonnei
showed higher antibiotic resistance and multidrug resistance compared to
S. flexneri
. The high level of resistance to ciprofloxacin highlights the need for more prudent use of this antibiotic and improved hygiene and sanitation. The study emphasized the importance of regular monitoring of drug resistance to effectively manage
Shigella
infections. These findings may provide the epidemiological evidence for conducting future appropriate
Shigella
vaccine clinical trials in Bangladesh.

IMPORTANCE

This nationwide study in Bangladesh assessed
Shigella
infections from 2014 to 2022 from clinical samples.
S. flexneri
was predominant, with concerning antibiotic resistance, notably to ciprofloxacin and nalidixic acid in over 96% of isolates. This emphasizes the urgency of prudent antibiotic use and improved hygiene. The findings provide crucial antimicrobial resistance patterns of
Shigella
species, highlighting the need for ongoing resistance monitoring and potentially informing future vaccine trials.
Identification and biological characteristics of
Fusarium tobaccum
sp. nov., a novel species causing tobacco root rot in Jilin Province, China
Authors: Xie Zhao , Gao Chong , Zhang Xiaoyan , Du Mengzhu , Wang Jun , Wang Xue , Lu Baohui , Chen Changqing , Yang Lina , Zhang Yanjing , Gao Jie 
Published: November 2024

ABSTRACT

Fusarium wilt of tobacco (FWT), caused by
Fusarium
spp., has emerged as a severe threat to tobacco production in China. In all, 132 isolates of
Fusarium
were isolated from tobacco and pathogenic to tobacco-causing FWT in Jilin Province, China. In this study, we identified 7 of 132 isolates as a novel species
Fusarium tobaccum
sp. nov. Zhao Xie & Jie Gao, using multi-gene phylogenetic analyses of translation elongation factor (
tef1
), β-tubulin (
tub2
), calmodulin (
cmdA
), and RNA polymerase II second largest subunit (
rpb2
) genes, along with subtle morphological differences. Isolates of
F. tobaccum
sp. nov. were clustered in a distinct branch in the maximum parsimony phylogenetic tree generated from the sequences of
tef1-rpb2-tub2-cmdA
and can be distinguished from closely related species
F. cugenangense
,
F. callistephi
, and
F. elaeidis
. The morphological characteristics of
F. tobaccum
sp. nov. are distinct from other
Fusarium
species.
F. tobaccum
sp. nov. exhibits abundant aerial mycelia and pigment production on potato dextrose agar (PDA), microconidia with 0–1 septa, and macroconidia with 2–5 septa on carnation leaf-piece agar (CLA), and produces abundant chlamydospores on Spezieller Nährstoffarmer agar (SNA) and CLA. The mycelia of
F. tobaccum
exhibited optimal growth at a pH of 7.1 and a temperature of 23.6°C. Sucrose and NaNO
3
significantly promoted the mycelial growth of
F. tobaccum
. PD medium was optimal for total sporulation. However, the sporulation ratios of the macrospores of
F. tobaccum
in PD, SN, and CMC were relatively low (0.48%, 2.51%, and 2.16%, respectively). These findings provided valuable insights into the morphological and biological characteristics of
F. tobaccum
.

IMPORTANCE

Fusarium
wilt of tobacco (FWT) is a prevalent issue in tobacco-growing regions globally, leading to significant losses in yield and quality. This study identified
F. tobaccum
sp. nov., a novel species of
Fusarium
causing FWT in China. The identification was based on multi-gene phylogenetic analyses and morphological characteristics. The effects of temperature, pH, carbon source, nitrogen source, medium, and light on the mycelial growth of
F. tobaccum
sp. nov. were determined. These findings might contribute to future research on the pathogenic mechanisms of this novel species and the development of strategies to control FWT.
Shifts in bacterial community composition during symbiotic seed germination of a terrestrial orchid and effects on protocorm development
Authors: Zhao Zeyu , Yang Luna , Wang Yaoyao , Qian Xin , Ding Gang , Jacquemyn Hans , Xing Xiaoke 
Published: November 2024

ABSTRACT

Fungi and bacteria often occupy very similar niches; they interact closely with each other, and bacteria can provide direct or indirect benefits to plants that form mutualistic interactions with fungi. In orchids, successful seed germination largely depends on compatible mycorrhizal fungi, but whether and how bacteria contribute to seed germination and protocorm development remains largely unknown. Here, we performed field and laboratory experiments to assess the potential role of bacteria in mediating seed germination and protocorm development in the terrestrial orchid
Gymnadenia conopsea
. Our results suggested that bacterial and fungal communities differ between developmental stages in the germination process. The diversity of bacterial and fungal communities and their interaction network in germinating seeds (Stage 1) differed significantly from those in later developmental stages (Stages 2–5).
Pseudomonas
gradually became the dominant bacterial group as the protocorms matured and showed a positive association with Ceratobasidiaceae fungi. Seed germination tests
in vitro
demonstrated that co-inoculation of
Ceratobasidium
sp. GS2 with
Pseudomonas
isolates significantly improved protocorm growth and development, suggesting that the observed increase in
Pseudomonas
abundance during protocorm development directly or indirectly improves the growth of germinating seeds. Overall, our findings indicate that bacteria may exert non-negligible effects on seed germination of orchids and, therefore, offer valuable perspectives for future strategies for conservation and cultivating orchid species.

IMPORTANCE

It is well known that orchid seeds depend on mycorrhizal fungi to supply the necessary nutrients that support germination in natural environments. Apart from fungi, bacteria may also be involved in the germination process of orchid seeds, but so far, their role has not been intensively studied. This research provides evidence that bacterial community composition changes during seed germination of the terrestrial orchid
Gymnadenia conopsea
. Interestingly,
in vitro
experiments showed that
Pseudomonas
spp., which were the most dominant bacteria in the later germination stages, improved protocorm growth. These results suggest that bacteria contribute to the germination of orchid seeds, which may open new perspectives to apply bacteria as a biofertilizer in the introduction and restoration of
G
.
conopsea
populations.
Short-term weight variability in infants and toddlers: an observational study
Authors: Wright Charlotte Margaret , Hope-McGill Ford , Sivakanthan Harshine , Cole Tim J 
Published: November 2024

AimsTo explore short-term weight variability in young children; (1) how it relates to expected weight gain and (2) how it is affected by age, time of day and dietary intakes and outputs.MethodsTwenty healthy infants aged 2–10 months and 21 healthy toddlers aged 12–35 months were weighed at home by their parents six times over 3 days. The toddlers’ parents also recorded whether they had eaten, drunk, urinated or passed stool in the previous 2 hours. The primary outcome was ‘noise’: the within-subject weight SD pooled separately for infants and toddlers, compared with their expected weight gain over 4 or 8 weeks. Analysis by successive pairs of weights was used to assess the extent of short-term weight gain and loss associated with time of day and eating, drinking and excretion.ResultsIn infants, noise (117 g) was much less than the expected weight gain over 4 weeks (280–1040 g) but in toddlers, noise (313 g) was higher than the expected gain over 4 weeks (180–230 g) and around three-quarters the expected gain over 8 weeks (359–476 g). In toddlers, weight tended to fall overnight and rise by day, and recent eating and passage of stool were associated with increased weight gain, even after adjustment for time of day.ConclusionsIn toddlers, the recorded weight may be 300 g higher or lower than the underlying weight trajectory, so that their weight gain based on measurements collected fewer than 8 weeks apart will often be misleading.
Association between RDW-SD and prognosis across glycemic status in patients with dilated cardiomyopathy
Authors: Feng Jiayu , Huang Yani , Huang Liyan , Zhao Xuemei , Li Xinqing , Xin Anran , Wang Chengyi , Zhang Yuhui , Zhang Jian 
Published: November 2024

IntroductionThe prognostic significance of red cell distribution width-SD (RDW-SD) as a promising inflammatory biomarker in individuals with non-ischemic dilated cardiomyopathy (DCM) and varying glycemic status remains unexplored.Research design and methodsPatients hospitalized for DCM in Fuwai Hospital from 2006 to 2021 were retrospectively included. The primary outcome encompassed all-cause mortality and heart transplantations. The multivariable Cox regression was used to evaluate the association between RDW-SD and outcomes in the overall DCM population, and among patients with normoglycemia (NG), pre-diabetes mellitus (pre-DM) and DM.ResultsAmong 1,102 patients with DCM, the median age was 48 years and 23.5% were women. In the overall DCM cohort, the RDW-SD was independently associated with the primary outcome (adjusted HR 1.29, 95% CI 1.15 to 1.45, p<0.001, per SD increase). When stratifying patients with glycemic status, the RDW-SD exhibited an independent association with outcome in patients with DCM with pre-DM and DM, the adjusted HRs were 1.48 (95% CI 1.21 to 1.79, p<0.001) and 1.30 (95% CI 1.06 to 1.60, p=0.011) per SD increase, respectively. However, in patients with DCM and NG, the prognostic value of RDW-SD was insignificant, with an adjusted HR of 1.20 per SD increase (95% CI: 0.97 to 1.48, p=0.101).ConclusionsRDW-SD was independently associated with the outcome in patients with DCM with pre-DM and DM, suggesting potential individualized therapeutic targets for this subset of patients with DCM.
Predictors for colectomy in patients with acute severe ulcerative colitis: a systematic review and meta-analysis
Authors: Zheng Jieqi , Fan Zinan , Li Chao , Wang Daiyue , Zhang Shenghong , Chen Rirong 
Published: November 2024

ObjectivesAcute severe ulcerative colitis (ASUC) poses challenges to patient management owing to its high surgical rate. This study aimed to identify predictors of colectomy in patients with ASUC.DesignThis is a systematic review and meta-analysis.Data sourcesPubMed and Web of Science were searched up to April 2024.Eligibility criteriaStudies on the predictors of colectomy in adult patients with ASUC were eligible.Data extraction and synthesisTwo reviewers independently extracted the data using a prespecified data collection sheet. A qualitative synthesis was performed in tabular form. Random-effect meta-analyses were conducted using OR and 95% CI.ResultsForty-two studies were included in the systematic review. The reported variables can be categorised into biomarkers, auxiliary examination findings, demographic and clinical characteristics, and drug factors. Through meta-analysis, albumin (OR 0.39 (95% CI 0.26 to 0.59) per 1 g/dL increment, I2=0.0%), high C reactive protein level (2.63 (1.53 to 4.52), I2=29.6%), high erythrocyte sedimentation rate level (2.92 (1.39 to 6.14), I2=0.0%), low haemoglobin level (2.08 (1.07 to 4.07), I2=56.4%), fulfilling the Oxford criteria (4.42 (2.85 to 6.84), I2=0.0%), extensive colitis (1.85 (1.24 to 2.78), I2=47.5%), previous steroids (1.75 (1.23 to 2.50), I2=17.7%) or azathioprine (2.25 (1.28 to 3.96), I2=0.0%) use, and sarcopenia (1.90 (1.04 to 3.45), I2=0.0%) were identified as valuable predictors for colectomy within 1 year. The ulcerative colitis endoscopic index of severity (OR 2.41 (95% CI 1.72 to 3.39), I2=1.5%) was the only predictor found to predict colectomy over 1 year.ConclusionIdentification of these predictors may facilitate risk stratification of patients with ASUC, drive personalised treatment and reduce the need for colectomy.
Approaches, enablers and barriers to govern the private sector in health in low- and middle-income countries: a scoping review
Authors: Goodman Catherine , Witter Sophie , Hellowell Mark , Allen Louise , Srinivasan Shuchi , Nixon Swapna , Burney Ayesha , Bhattacharjee Debrupa , Cocozza Anna , Appleford Gabrielle , Thabet Aya , Clarke David 
Published: November 2024

IntroductionThe private sector plays a substantial role in delivering and financing healthcare in low- and middle-income countries (LMICs). Supporting governments to govern the private sector effectively, and so improve outcomes across the health system, requires an understanding of the evidence base on private health sector governance. This paper reports on a scoping review, which synthesised evidence on the approaches used to govern private sector delivery and financing of healthcare in LMICs, the effectiveness of these approaches and the key enablers and barriers to strengthening governance.MethodsWe undertook a systematic search of databases of published articles and grey literature to identify eligible papers published since 2010, drawing on WHO’s governance definition. Data were extracted into a pretested matrix and analysed using narrative synthesis, structured by WHO’s six governance behaviours and an additional cross-cutting theme on capacities.Results107 studies were selected as relevant, covering 101 LMICs. Qualitative methods and document/literature review were predominant. The findings demonstrate the relevance of the WHO governance behaviours, but the lack of robust evidence for approaches to implementing them. Valuable insights from the literature include the need for a clear vision around governance aims; the importance of ensuring that policy dialogue processes are inclusive and transparent, avoiding interest group capture; the benefits of exploiting synergies between governance mechanisms; and the need to develop capacity to enact governance among both public and private actors.ConclusionGovernance choices shape not just the current health system, but also its future development. Common barriers to effective governance must be addressed in policy design, stakeholder engagement, public and private sector accountability, monitoring and capacity. Achieving this will require in-depth explorations of governance mechanisms and more rigorous documentation of implementation and outcomes in diverse contexts.
Predictors of study dropout in cognitive-behavioural therapy with a trauma focus for post-traumatic stress disorder in adults: An individual participant data meta-analysis
Authors: Wright Simonne , Karyotaki Eirini , Cuijpers Pim , Bisson Jonathan , Papola Davide , Witteveen Anke B , Back Sudie E , Bichescu-Burian Dana , Capezzani Liuva , Cloitre Marylene , Devilly Grant J , Elbert Thomas , Mello Marcelo , Ford Julian D , Grasso Damion , Gamito Pedro , Gray Richard , Haller Moira , Hunt Nigel , Kleber Rolf J , König Julia , Kullack Claire , Laugharne Jonathan , Liebman Rachel , Lee Christopher William , Lely Jeannette , Markowitz John C. , Monson Candice , Nijdam Mirjam J , Norman Sonya B , Olff Miranda , Orang Tahereh Mina , Ostacoli Luca , Paunovic Nenad , Petkova Eva , Resick Patricia , Rosner Rita , Schauer Maggie , Schmitz Joy M , Schnyder Ulrich , Smith Brian N. , Vujanovic Anka A , Zang Yinyin , Duran Érica Panzani , Neto Francisco Lotufo , Seedat Soraya , Sijbrandij Marit 
Published: November 2024

BackgroundAvailable empirical evidence on participant-level factors associated with dropout from psychotherapies for post-traumatic stress disorder (PTSD) is both limited and inconclusive. More comprehensive understanding of the various factors that contribute to study dropout from cognitive-behavioural therapy with a trauma focus (CBT-TF) is crucial for enhancing treatment outcomes.ObjectiveUsing an individual participant data meta-analysis (IPD-MA) design, we examined participant-level predictors of study dropout from CBT-TF interventions for PTSD.MethodsA comprehensive systematic literature search was undertaken to identify randomised controlled trials comparing CBT-TF with waitlist control, treatment-as-usual or another therapy. Academic databases were screened from conception until 11 January 2021. Eligible interventions were required to be individual and in-person delivered. Participants were considered dropouts if they did not complete the post-treatment assessment.FindingsThe systematic literature search identified 81 eligible studies (n=3330). Data were pooled from 25 available CBT-TF studies comprising 823 participants. Overall, 221 (27%) of the 823 dropped out. Of 581 civilians, 133 (23%) dropped out, as did 75 (42%) of 178 military personnel/veterans. Bivariate and multivariate analyses indicated that military personnel/veterans (RR 2.37) had a significantly greater risk of dropout than civilians. Furthermore, the chance of dropping out significantly decreased with advancing age (continuous; RR 0.98).ConclusionsThese findings underscore the risk of premature termination from CBT-TF among younger adults and military veterans/personnel.Clinical implicationUnderstanding predictors can inform the development of retention strategies tailored to at-risk subgroups, enhance engagement, improve adherence and yield better treatment outcomes.
Improving the primary care clinical testing process in southwest Scotland: a systems-based approach
Authors: Howson Alex , Ishmael Richard 
Published: November 2024

IntroductionAcross all healthcare environments, inadequately specified patient test requests are commonly encountered and can lead to wasted clinician time and healthcare resources, in addition to either missed or unnecessary testing taking place.Before this work, in a general practice in Southwest Scotland, a mean value of 42% of test requests were already uploaded to ordercomms (a widely used system in general practice for designating clinical testing instructions) at patient presentation, leaving an opportunity for error and wasted clinician time/resources.MethodsPatient appointment records were retrospectively reviewed in a general practice in Southwest Scotland to monitor the proportion of test requests already uploaded to ordercomms at the time of patient presentation.The use of quality improvement tools and plan-do-study-act cycling allowed the testing of four change ideas attributable to different ‘pathways’ of origin for test requests.Change ideas included increasing clinician and secondary care/docman origin test requests already on ordercomms prior to patient presentation, reducing patient origin test requests and improving the test requesting system.ResultsThe percentage of test requests already on ordercomms at patient presentation increased from a mean of 42% to 89% over a 30 week test period. The use of test pre-set templates was a welcome intervention that was agreed to be made accessible to 30+ regional general practices.ConclusionThe use of pre-set templates for clinical testing encouraged a 47% rise in test requests already uploaded to ordercomms prior to patient presentation. This saved up to 90 min of clinician time weekly and ensured patients received the correct tests at the appropriate time.Our findings supported the use of pre-set testing templates, in combination with effective information communication, and were recommended for use in any clinical environment requiring patient testing.