bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adaptation for
Staphylococcus aureus
to hosts via insertion mutation in the accessory gene regulator
agrC
gene: decreased virulence and enhanced persistence capacity
Authors: Chen Jiawei , Wu Yun , Zhu Ying , Zhang Li , Xu Yingchun , Liu Yali 
Published: November 2024

ABSTRACT

Staphylococcus aureus
is an important human pathogen due to its vast array of virulence factors regulated by multiple regulatory mechanisms, including the accessory gene regulator. In this study, two
S
.
aureus
strains were simultaneously isolated from the blood of a febrile patient, belonging to the same clone, designated as 23H with a complete hemolytic phenotype, and 23B, exhibiting an incomplete hemolytic phenotype. The genomic comparison between strains 23B and 23H revealed that 23B had a single adenine base insertion at position 923 in the
agrC
gene, leading to a functional loss of the encoded AgrC. Experimental findings showed that strain 23B had decreased hemolytic activity, lower cytotoxicity against human alveolar epithelial A549 cells and in the
Galleria mellonella
model, and a reduced ability to survive intracellularly after infecting macrophages, in comparison to 23H. Conversely, 23B exhibited enhanced biofilm formation, greater adherence to A549 cells, and increased persistence in the face of vancomycin and daptomycin treatment. Transcriptomic analysis revealed that 23B upregulated surface protein-encoding genes while simultaneously reducing the expression levels of virulence factors, highlighting the intricate regulatory adjustments facilitating its persistence and reducing pathogenic potential. ATP assay results indicated that 23B maintained elevated ATP levels during the exponential phase yet exhibited reduced levels in the stationary phase when compared with 23H. Our findings suggested that the mutation in the
agrC
gene of
S. aureus
results in diminished virulence but markedly enhances persistence. This mutated strain warrants clinical attention because it may lead to treatment failures and persist in patients.

IMPORTANCE

In clinical antimicrobial therapy, bacterial strains often develop resistance to antimicrobial agents. Additionally, mutations in their gene regulatory networks can increase their persistence, especially in immunocompromised patients. This study identified an insertion mutation in the accessory gene regulator,
agrC
gene, carried by a
Staphylococcus aureus
strain isolated from the blood of a febrile patient, leading to the functional loss of AgrC. Further research revealed that despite the reduced virulence of the mutated strain, it significantly bolstered the capacity to adapt and endure within the host during prolonged infections. This was evidenced by increased adhesion and biofilm formation capabilities, development of antimicrobial tolerance, and decreased ATP levels linked to persistence. Therefore, monitoring these mutations in
S. aureus
is crucial clinically, as they can complicate treatment strategies.
Development of SacB-based counterselection for efficient allelic exchange in
Fusobacterium nucleatum
Authors: Zhou Peng , G C Bibek , Hu Bo , Wu Chenggang 
Published: November 2024

ABSTRACT

Fusobacterium nucleatum
, prevalent in the oral cavity, is significantly linked to overall human health. Our molecular comprehension of its role in oral biofilm formation and its interactions with the host under various pathological circumstances has seen considerable advancements in recent years, primarily due to the development of various genetic tools for DNA manipulation in this bacterium. Of these, counterselection-based unmarked in-frame mutation methods have proved notably effective. Under suitable growth conditions, cells carrying a counterselectable gene die, enabling efficient selection of rare, defined allelic exchange mutants. The
sacB
gene from
Bacillus subtilis
, encoding levansucrase, is a widely used counterselective marker partly due to the easy availability of sucrose. Yet, its potential application in
F. nucleatum
genetic study remains untested. We demonstrated that
F. nucleatum
cells expressing
sacB
in either a shuttle or suicide plasmid exhibit a lethal sensitivity to supplemental sucrose. Utilizing sucrose counterselection, we created an in-frame deletion of the
F. nucleatum tonB
gene, a critical gene for energy-dependent transport processes in Gram-negative bacteria, and a precise knock-in of the luciferase gene immediately following the stop codon of the
hslO
gene, the last gene of a five-gene operon possibly related to the natural competence of
F. nucleatum
. Post-counterselection with 5% sucrose, chromosomal plasmid loss occurred in all colonies, leading to gene alternations in half of the screened isolates. This
sacB
-based counterselection technique provides a reliable method for isolating unmarked gene mutations in wild-type
F. nucleatum
, enriching the toolkit for fusobacterial research.

IMPORTANCE

Investigations into
Fusobacterium nucleatum
’s role in related diseases significantly benefit from the strategies of creating unmarked gene mutations, which hinge on using a counterselective marker. Previously, the
galk
-based allelic exchange method, although effective, faced an inherent limitation—the need for a modified host. This study aims to surmount this limitation by substituting
galK
with
sacB
for gene modification in
F. nucleatum
. Our application of the
sacB
-based methodology successfully yielded a
tonB
in-frame deletion mutant and a luciferase gene knock-in at the precise chromosomal location in the wild-type background. The new method augments the existing toolkit for
F. nucleatum
research and has far-reaching implications due to the easy accessibility to the counterselection compound sucrose. We anticipate its broader adoption in further exploration, thereby reinforcing its critical role in propelling our understanding of
F. nucleatum
.
Gardenoside attenuates
Staphylococcus aureus
-induced mastitis by inhibiting inflammation and ferroptosis through Nrf2/SLC7A11/GPX4 signaling pathway
Authors: Sui Guoqing , Jiang Wei , Guan Lianyue 
Published: November 2024

ABSTRACT

The occurrence of mastitis is mainly due to the infection of mammary tissue by pathogens, which causes the inflammation of mammary tissue. Gardenoside (GAD), an iridoid active ingredient extracted from
Gardenia Jasminoides Ellis
, has been revealed to exhibit anti-inflammatory and anti-oxidative roles. However, the therapeutic effect of GAD on mastitis remains unclear. Our aim was to identify the therapeutic effect of GAD on
Staphylococcus aureus (S. aureus
)-induced mastitis and clarify its mechanism. To carry out this work,
S. aureus
-induced mastitis of mice model was established. Enzyme-Linked Immunosorbent Assay (ELISA) was conducted to detect the production of Interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α). The biochemical method was used to detect the antioxidant factors glutathione (GSH), malondialdehyde (MDA), and iron content. Western blot was used to detect the expression of Nrf2/SLC7A11/GPX4 signal-related proteins. The results demonstrated that GAD alleviated Myeloperoxidase (MPO) activity, IL-1β and TNF-α production, and NF-κB activation. MDA and iron contents were also inhibited by GAD. Meanwhile, GSH level and GPX4, SLC7A11, and ferritin expressions were increased by GAD treatment. In addition, the expressions of Nrf2 and HO-1 were upregulated by GAD. In conclusion, GAP may inhibit
S. aureus
-induced mastitis in mice by triggering the Nrf2/SLC7A11/GPX4 signaling pathway and alleviating inflammation and ferroptosis.

IMPORTANCE

Mastitis, as an important disease that endangers the development of the dairy industry, causes huge economic losses to the breeding industry.
Staphylococcus aureus
is one of the important pathogenic bacteria that cause mastitis. Antibiotics are considered to be the first choice in the treatment of the
S. aureus
-induced mastitis. However, the overuse of antibiotics leads to bacterial resistance and antibiotic residues. Therefore, this study explored whether effective extracts of traditional herbs could be used as alternatives to antibiotics.
Alkalothermophilic Iron-Reducing Bacteria of the Goryachinsk Thermal Water Basin
Authors: Zavarzina D. G. , Klyukina A. A. , Merkel A. Y. , Maslova T. A. , Maslov A. A. 
Published: November 2024

Abstract
A study of iron-reducing prokaryotes that use the poorly crystalline mineral ferrihydrite as an electron acceptor revealed their widespread occurrence on the planet. However, the ability of iron reducers to develop under polyextreme conditions (at elevated values of pH and temperature) has not been previously demonstrated. To confirm the existence of alkalothermophilic iron reducers, we studied the water and sediment samples from the Goryachinsk nitrogen-rich thermal water basin. These springs are associated with young tectonic fractures in the Baikal rift zone; their water is characterized by low salinity, alkaline pH (8.8‒9.2) and temperature of 53‒55°C. Enrichment cultures reducing synthesized ferrihydrite were obtained by adding this mineral to the water and sediment samples from the Goryachinsk thermal springs, followed by anaerobic incubation at 50 and 55°C. The 16S rRNA gene profiling of the water and sediment samples and of the primary enrichment cultures revealed high taxonomic diversity, almost exclusively represented by bacterial taxa. Subsequent transfers with ferrihydrite and organic acids or hydrogen as electron donors resulted in stable enrichment cultures of organo- and lithotrophic alkalothermophilic iron reducers. Members of the genus Parvivirga, one of the first cultured representatives of the OPB41 group (now the order Anaerosomatales, phylum Actinomycetota), constituted 30 to 50% of the total abundance.
National survey on the prevalence of single-gene aetiologies for genetic developmental and epileptic encephalopathies in Italy
Authors: Mei Davide , Balestrini Simona , Parrini Elena , Gambardella Antonio , Annesi Grazia , De Giorgis Valentina , Gana Simone , Bassi Maria Teresa , Zucca Claudio , Elia Maurizio , Vetri Luigi , Castellotti Barbara , Ragona Francesca , Mastrangelo Mario , Pisani Francesco , d'Orsi Giuseppe , Carella Massimo , Pruna Dario , Giglio Sabrina , Marini Carla , Cesaroni Elisabetta , Riva Antonella , Scala Marcello , Licchetta Laura , Minardi Raffaella , Contaldo Ilaria , Gambardella Maria Luigia , Cossu Alberto , Proietti Jacopo , Cantalupo Gaetano ,   LICE Collaborative Group, Trivisano Marina , De Dominicis Angela , Specchio Nicola , Tassi Laura , Guerrini Renzo 
Published: November 2024

Background
We aimed to estimate real-world evidence of the prevalence rate of genetic developmental and epileptic encephalopathies (DEEs) in the Italian population over a 11-year period.

Methods
Fifteen paediatric and adult tertiary Italian epilepsy centres participated in a survey related to 98 genes included in the molecular diagnostic workflows of most centres. We included patients with a clinical diagnosis of DEE, caused by a pathogenic or likely pathogenic variant in one of the selected genes, with a molecular diagnosis established between 2012 and 2022. These data were used as a proxy to estimate the prevalence rate of DEEs.

Results
We included 1568 unique patients and found a mean incidence proportion of 2.6 patients for 100.000 inhabitants (SD=1.13) with consistent values across most Italian regions. The number of molecular diagnoses showed a continuing positive trend, resulting in more than a 10-fold increase between 2012 and 2022. The mean age at molecular diagnosis was 11.2 years (range 0–75). Pathogenic or likely pathogenic variants in genes with an autosomal dominant inheritance pattern occurred in 77% (n=1207) patients; 17% (n=271) in X-linked genes and 6% (n=90) in genes with autosomal recessive inheritance. The most frequently reported genes in the survey wereSCN1A(16%), followed byKCNQ2(5.6%) andSCN2A(5%).

Conclusion
Our study provides a large dataset of patients with monogenic DEE, from a European country. This is essential for informing decision-makers in drug development on the appropriateness of initiatives aimed at developing precision medicine therapies and is instrumental in implementing disease-specific registries and natural history studies.
Occupational risk of salmonellosis and campylobacteriosis: a nationwide population-based registry study
Authors: Duijster Janneke W , Franz Eelco , Neefjes Jacques J C , Mughini-Gras Lapo 
Published: November 2024

Objectives
Occupational exposure to animals and foods thereof is a poorly characterised risk factor for salmonellosis and campylobacteriosis, the main causes of bacterial gastroenteritis in the Western world. We performed a population-based registry study in the Netherlands to assess whether differences exist in the incidence of reported salmonellosis and campylobacteriosis cases among occupational groups, and whether they can be explained by differences in the magnitude of exposure to these pathogens, as defined by serology.

Methods
Person-level occupational data for all Dutch residents were linked to lab-confirmed salmonellosis and campylobacteriosis data, and to serological data from a previous national serosurvey. SIRs for salmonellosis and campylobacteriosis among occupational sectors and specific high-risk occupations were calculated based on the total employed population. Moreover,SalmonellaandCampylobacterseroincidence rates were compared among sectors and high-risk occupations.

Results
Occupational exposure to live animals or manure and working in the sale of animal-derived food products were associated with significantly increased risks of salmonellosis (SIR 1.55–1.82) and campylobacteriosis (SIR 1.36–1.65). Moreover, incidences were significantly higher in specific industrial sectors, as well as healthcare and social work sectors. Mean seroincidence rates ranged from 1.28 to 2.30 infections/person-year forCampylobacter, and from 0.36 to 0.99 forSalmonella, with only slightly higher rates for people in high-risk occupations.

Conclusions
Significant differences in reported salmonellosis and campylobacteriosis incidence exist among occupational sectors, with the highest incidence in those persons occupationally exposed to live animals. These differences are only partially reflected in the serology.
Oropharyngeal gonorrhoea among heterosexual men and women at a sexual health centre in Rotterdam, the Netherlands, 2023: reservoir for transmission?
Authors: Twisk Denise E , Klaassen Corné , van Westreenen Mireille , Götz Hannelore M 
Published: November 2024

BackgroundSexual health centres (SHCs) in the Netherlands report a surge in gonorrhoea, especially among young women (notably oropharyngeal) and men who have sex with women (MSW) since the second half of 2022. MSW are not routinely oropharyngeal tested, and women only when reporting oral sex. This cross-sectional study aimed to assess oropharyngeal gonorrhoea in MSW and women, and potential underdiagnosis.MethodsFrom 10 August to 10 November 2023, the SHC in Rotterdam, the Netherlands, extended its gonorrhoea testing protocol, requiring oropharyngeal tests for all MSW and women. Positive cobas nucleic acid amplification test (NAAT) results were followed by culture sampling. Oropharyngeal infections were confirmed with a second NAAT (opa gene-based PCR), and for discrepancies a third NAAT (GeneXpert CT/NG test) was employed. The impact of extended testing on detection rates, along with the corresponding 95% CIs, was analysed.ResultsThe overall gonorrhoea detection rate was 6.4% (95% CI 4.7% to 8.8%) among MSW and 6.0% (95% CI 4.8% to 7.6%) among women, compared with 3.6% (95% CI 2.3% to 5.4%) and 6.0% (95% CI 4.8% to 7.6%) without expanded testing. Oropharyngeal rates were 6.4% (95% CI 4.4% to 9.2%) for MSW and 4.3% (95% CI 3.2% to 5.7%) for women. Highest positivity was among individuals notified, <25 years, without migratory background, with lower educational levels and more sex partners. Oropharyngeal cultures confirmed viable gonorrhoea in 39.1% of MSW and 35.5% of women. False positives were 7.4% among MSW and 10.8% among women. Confirmed oropharyngeal gonorrhoea positivity rate was 5.9% (95% CI 4.0% to 8.6%) among MSW and 3.9% (95% CI 2.8% to 5.2%) among women.ConclusionOropharyngeal gonorrhoea is common and currently underdiagnosed among MSW. The impact of this underdiagnosis on transmission dynamics under the current testing policy remains unclear. Further research is needed to inform prevention and control strategies, especially given the recent surge in gonorrhoea.
Economic costs of tobacco-related diseases in Hong Kong in 2021
Authors: Ng Carmen S , Yu Coco Wing Sze , Leung Lancelot , Wong Eponine Kate , Ho Sai Yin , Ip Dennis K M , Wu Yongda , Wang Man Ping , Quan Jianchao 
Published: November 2024

BackgroundHong Kong has one of the lowest smoking prevalence both within China and among high-income economies. As tobacco use consistently declined over the past decades, we examine whether there are corresponding cost reductions.MethodsData were sourced from diverse population-wide datasets including government reports and public hospital records. Costs were calculated using Global Burden of Disease (GBD) 2019 risk estimates for active smoking. Direct costs encompassed public and private healthcare expenses, while indirect costs included the value of years of productive life lost, days off work due to active smoking or secondhand smoke exposure, and long-term care costs.FindingsActive smoking accounted for 26.3% of deaths in people aged 35 or over. Healthcare costs amounted to US$342 million and US$45 million for active and secondhand smoking. Annual tobacco-related diseases reached US$1.27 billion (0.3% of 2021 Hong Kong GDP). Compared with previous methods, the analysis using GBD 2019 risk estimates showed a twofold increase in lives lost due to active smoking but a 31.0% decrease for secondhand smoking.InterpretationPast studies greatly underestimate the health burden of tobacco compared with more recent data on the wider risks. Despite a decline in smoking prevalence, the total costs associated with smoking have risen as utilisation shifts from primary care towards more expensive specialist care. The long-term health and economic impacts of tobacco use remain substantial even in regions of China that have now achieved low smoking prevalence.
Assessing causal relationships between diabetes mellitus and idiopathic pulmonary fibrosis: a Mendelian randomisation study
Authors: Moss Samuel T , Minelli Cosetta , Leavy Olivia C , Allen Richard J , Oliver Nick , Wain Louise V , Jenkins Gisli , Stewart Iain 
Published: November 2024

BackgroundIdiopathic pulmonary fibrosis (IPF) is a disease of progressive lung scarring. There is a known association between diabetes mellitus (DM) and IPF, but it is unclear whether a causal relationship exists between these traits.ObjectivesThe objectives of this study are to examine causal relationships among DM, diabetes-associated traits and IPF using a Mendelian randomisation approach.MethodsTwo-sample MR approaches, including bidirectional inverse-variance weighted random effects and routine sensitivity models, used genetic variants identified from genome-wide association studies for type 1 diabetes (T1D), type 2 diabetes (T2D), glycated haemoglobin level (HbA1c), fasting insulin level and body mass index (BMI) to assess for causal effects of these traits on IPF. Further analyses using pleiotropy-robust and multivariable MR (MVMR) methods were additionally performed to account for trait complexity.ResultsResults did not suggest that either T1D (OR=1.00, 95% CI 0.93 to 1.07, p=0.90) or T2D (1.02, 0.93 to 1.11, p=0.69) are in the causal pathway of IPF. No effects were suggested of HbA1c (1.19, 0.63 to 2.22, p=0.59) or fasting insulin level (0.60, 0.31 to 1.15, p=0.12) on IPF, but potential effects of BMI on IPF were indicated (1.44, 1.12 to 1.85, p=4.00×10−3). Results were consistent in MVMR, although no independent effects of T2D (0.91, 0.68 to 1.21, p=0.51) or BMI (1.01, 0.94 to 1.09, p=0.82) on IPF were observed when modelled together.ConclusionsThis study suggests that DM and IPF are unlikely to be causally linked. This comorbid relationship may instead be driven by shared risk factors or treatment effects.
A framework for simultaneous fit of QCD and BSM parameters with xFitter
Authors: Shen Xiao-Min , Amoroso Simone , Gao Jun , Lipka Katerina , Zenaiev Oleksandr 
Published: November 2024

AbstractAn extension of the xFitter open-source program for QCD analyses is presented, allowing for a polynomial parameterization of the dependence of physical observables on theoretical parameters. This extension enables simultaneous determination of parton distribution functions (PDFs) and new physics parameters within the framework of the Standard Model Effective Field Theory (SMEFT). The functionalities of the code are illustrated in a sensitivity study, where a simultaneous determination of the PDFs, top quark mass and the couplings of selected dimension-6 SMEFT operators is addressed using projections for measurements of top quark-antiquark pair production at the High-Luminosity LHC. The importance of considering all the correlations of the parton distributions, top quark mass and the SMEFT parameters in a simultaneous QCD+SMEFT analysis is demonstrated. This work serves as a new platform for simultaneous extraction of the PDFs and the SM/SMEFT parameters based on xFitter.
Analyzing variable characteristics effects on an unsteady hybrid nanofluid flow over a rotating sphere near a stagnation point with thermal stratification — A comparative study
Authors: Li Shuguang , Shahmir Nazia , Ramzan Muhammad , Alkarni Shalan , Kadry Seifedine 
Published: November 2024

Efficient dissipation of heat is crucial in various heat transfer applications. Hybrid nanofluids outperform conventional coolants in both absorbing and transferring heat, rendering them ideal for cooling purposes in machinery, electronics, and various industrial processes. Given these intriguing properties of coolant-based hybrid nanofluid, this numerical study aims to analyze the unsteady flow of hybrid nanofluid around a rotating sphere with thermal stratification, and variable heat source and sink effects. This investigation incorporates aluminum alloys AA7072 and AA7075 as nanoparticles in the Fluorinert liquid named FC-72 base liquid. The AA7072 alloy is a composition of silicon, ferrous, and copper added to aluminum and zinc in the ratios of 98:1. Similarly, AA7075 comprises a combination of aluminum [Formula: see text], zinc [Formula: see text], magnesium [Formula: see text], and copper [Formula: see text], together with magnesium and silicon ferrous. What sets this model apart is its incorporation of variable porosity and permeability, along with temperature-dependent viscosity and thermal conductivity. The governing equations are converted into systems of differential equations, and a boundary value problem solver for ordinary differential equations of fourth order using the collocation (bvp4c) technique is employed to obtain the numerical solution. Two alternative scenarios for porous media — (i) constant porosity and permeability, and (ii) variable porosity and permeability — are determined for relevant parameters versus the velocity and temperature profiles. Additionally, the heat transfer rate is computed versus numerous parameters. It is perceived that secondary velocity profiles decrease more significantly with higher estimates of the variable viscosity parameter when a constant porous medium is assumed. Furthermore, the heat transfer rate of the FC-72-based hybrid nanofluid increases with higher estimates of the rotation parameter and the particle volume fraction of aluminum alloys.