bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significant increase of CTX-M-15-ST131 and emergence of CTX-M-27-ST131 Escherichia coli high-risk clones causing healthcare-associated bacteraemia of urinary origin in Spain (ITUBRAS-2 project)
Authors: Becerra-Aparicio Federico , Gómez-Zorrilla Silvia , Hernández-García Marta , Gijón Desiré , Siverio Ana , Berbel Dàmaris , Sánchez-Carrillo Carlos , Cercenado Emilia , Rivera Alba , de Malet Ana , Xercavins Mariona , Ruiz de Gopegui Enrique , Canoura-Fernández Luis , Martínez José Antonio , Seral Cristina , Del Pozo José Luis , Cotarelo Manuel , Díaz-Regañón Jazmín , Cantón Rafael , Oliver Antonio , Horcajada Juan Pablo , Ruiz-Garbajosa Patricia 
Published: August 2023

Abstract

Objectives
To assess the microbiological characteristics of Escherichia coli causing healthcare-associated bacteraemia of urinary origin (HCA-BUO) in Spain (ITUBRAS-2 project), with particular focus on ESBL producers and isolates belonging to ST131 high-risk clone (HiRC). Clinical characteristics and outcomes associated with ST131 infection were investigated.

Methods
A total of 222 E. coli blood isolates were prospectively collected from patients with HCA-BUO from 12 tertiary-care hospitals in Spain (2017–19). Antimicrobial susceptibility and ESBL/carbapenemase production were determined. ST131 subtyping was performed. A subset of 115 isolates were selected for WGS to determine population structure, resistome and virulome. Clinical charts were reviewed.

Results
ESBL-producing E. coli prevalence was 30.6% (68/222). ST131 represented 29.7% (66/222) of E. coli isolates and accounted for the majority of ESBL producers (46/68, 67.6%). The C2/H30-Rx subclone accounted for most ST131 isolates (44/66) and was associated with CTX-M-15 (37/44) and OXA-1 enzymes (27/44). Cluster C1-M27 was identified in 4/10 isolates belonging to subclade C1/H30-R1 and associated with CTX-M-27. Additionally, ST131 isolates showed a high content of other acquired resistance genes, and clade C/ST131 isolates carried characteristic QRDR mutations. They were categorized as uropathogenic E. coli and had higher aggregate virulence scores. ST131 infection was associated with more complex patients, prior use of cephalosporins and inadequate empirical treatment but was not associated with worse clinical outcomes.

Conclusions
ST131 HiRC is the main driver of ESBL-producing E. coli causing HCA-BUO in Spain, mainly associated with the expansion of subclade CTX-M-15-C2/H30-Rx and the emergence of CTX-M-27-C1/H30-R1 (Cluster C1-M27).
Blood telomere length gain in people living with HIV switching to dolutegravir plus lamivudine versus continuing triple regimen: a longitudinal, prospective, matched, controlled study
Authors: Lombardi Francesca , Sanfilippo Alessia , Fabbiani Massimiliano , Borghetti Alberto , Ciccullo Arturo , Tamburrini Enrica , Di Giambenedetto Simona 
Published: August 2023

Abstract

Background
Blood telomere length (BTL) is a validated biomarker of aging. ART reduces immunosenescence and has benefits in terms of BTL in people living with HIV (PLWH). However, it has also been observed that ART containing NRTIs, such as tenofovir or abacavir, which are potent inhibitors of human telomerase activity in vitro, might negatively affect BTL. Here we investigated the effects on BTL 1 year after switching to a dual therapy (DT) with dolutegravir + lamivudine versus maintaining a standard triple therapy (TT) with a two-NRTI backbone and an anchor drug.

Methods
This was a longitudinal, prospective, matched, controlled study that included virologically suppressed adults on stable three-drug ART who either switched at baseline (BL) to DT or maintained TT. The DT and TT groups were 1:1 matched for age, sex, years since HIV diagnosis, years on ART and anchor drug. BTL was assessed by a monochrome multiplex qPCR at BL and after 48 weeks (W48).

Results
We enrolled 120 PLWH, i.e. 60 participants in each group. At BL, the BTL means were comparable between the two groups (P = 0.973). At W48, viro-immunological status was stable and an overall increase in the mean BTL was observed, i.e., +0.161 (95%CI, 0.054–0.268) (P = 0.004). However, the within-group analysis showed a significant mean BTL gain in the DT group (P = 0.003) but not in the TT group (P = 0.656).

Conclusions
In this setting of virologically suppressed PLWH, simplifying to dolutegravir + lamivudine was associated with a higher gain in BTL than maintaining triple therapy after the 1 year follow-up. These findings suggest that as a simplification strategy dolutegravir + lamivudine might have a positive effect on BTL.
The epidemiology and microbiological characteristics of infections caused by Gram-negative bacteria in Qatar: national surveillance from the Study for Monitoring of Antimicrobial Resistance Trends (SMART): 2017 to 2019
Authors: Sid Ahmed Mazen A , Petkar Hawabibee Mahir , Saleh Thoraya M , Albirair Mohamed , Arisgado Lolita A , Eltayeb Faiha K , Mahmoud Hamed Manal , Al-Maslamani Muna A , Al Khal Abdul Latif , Alsoub Hussam , Ibrahim Emad Bashir , Abdel Hadi Hamad 
Published: August 2023

Abstract

Background
The global Study of Monitoring Antimicrobial Resistance Trends (SMART) is a surveillance program for evaluation of antimicrobial resistance (AMR) in Gram-negative bacteria (GNB) from different regions including Gulf countries.

Objectives
To evaluate AMR in GNB from various clinical specimens including microbiological and genetic characteristics for existing and novel antimicrobials.

Methods
A prospective study was conducted on clinical specimens from Hamad Medical Corporation, Qatar, between 2017 and 2019 according to the SMART protocol. Consecutive GNB from different sites were evaluated including lower respiratory, urinary tract, intrabdominal and bloodstream infections.

Results
Over the 3 years study period, 748 isolates were evaluated from the specified sites comprising 37 different GNB outlining four key pathogens: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia.
For the two major pathogens E. coli and K. pneumoniae, phenotypic ESBL was identified in 55.77% (116/208) compared to 39% (73/187), while meropenem resistance was 3.8% compared to 12.8% and imipenem/relebactam resistance was 2.97% compared to 11.76%, respectively. The overall ceftolozane/tazobactam resistance for E. coli was 9.6% (20/208) compared to 14.97% (28/187) for K. pneumoniae while resistance for ceftazidime/avibactam was 3.65% (5/137) and 5.98% (10/117), respectively. Genomic characteristics of 70 Enterobacterales including 48 carbapenem-resistant, revealed prevalence of β-lactamases from all classes, predominated by blaCXM-15 while carbapenem resistance revealed paucity of blaKPC and dominance of blaOXA-48 and blaNDM resistance genes.

Conclusions
Surveillance of GNB from Qatar showed prevalence of key pathogens similar to other regions but demonstrated significant resistance patterns to existing and novel antimicrobials with different underlying resistance mechanisms.
WHO/INRUD prescribing indicators among tertiary regional referral hospitals in Dar es Salaam, Tanzania: a call to strengthen antibiotic stewardship programmes
Authors: Costantine Judith K , Bwire George M , Myemba David T , Sambayi Godfrey , Njiro Belinda J , Kilipamwambu Amosi , Ching’oro Novatus , Shungu Rehema S , Mganga Mathew , Majigo Mtebe V 
Published: August 2023

AbstractBackgroundAntibiotic prescribing should be guided by national essential medicines lists (NEMLs) and treatment guidelines; however, there are inadequate data on antibiotic utilization patterns in tertiary hospitals in Tanzania. This study aimed to determine antibiotic prescribing patterns in tertiary hospitals in Dar es Salaam, Tanzania.MethodsA retrospective cross-sectional study was conducted in three regional referral hospitals. About 200 prescription records from 2020 to 2022 were analysed at each hospital for prescribing patterns using WHO/ International Network of Rational Use of Drugs (INRUD) indicators (1993) and the AWaRe 2021 classification. Factors associated with receiving an antibiotic prescription were assessed using a logistic regression model. Facilities were ranked on prescribing practices using the index of rational drug prescribing (IRDP).ResultsA total of 2239 drugs were prescribed, of which 920 (41.1%) were antibiotics. An average of 3.7 ± 1.5 (optimal: 1.6–1.8) total medicines and 1.53 ± 0.78 antibiotics were prescribed per patient. About 88.0% (528) of the prescriptions contained antibiotics (optimal: 20.0%–26.8%), while 78.2% (413) of all antibiotic prescriptions contained injections (optimal: 13.4%–24.1%). Furthermore, 87.5% (462) of the antibiotics were prescribed in generic names (optimal: 100%), while 98.7% (521) conformed to the NEML (optimal: 100%). Metronidazole was the most frequently prescribed antibiotic (39.2%; n = 134), followed by ceftriaxone (37.1%, n = 127) and amoxicillin/clavulanic acid (8.5%, n = 29).ConclusionsWe found substantial empirical prescribing and overuse of antibiotics exceeding WHO recommendations. Antibiotic overuse varied across the hospitals. Being male, having underlying conditions such as diabetes mellitus, and/or being treated at Temeke hospital were associated with receiving an antibiotic prescription. We recommend strengthening antibiotic stewardship programmes in the studied facilities.
The CKD-EPI 2021 Equation and Other Creatinine-Based Race-Independent eGFR Equations in Chronic Kidney Disease Diagnosis and Staging
Authors: Lu Song , Robyak Kimberly , Zhu Yusheng 
Published: August 2023

Abstract

Background
Recent debate on the race correction factor in creatinine-based estimated glomerular filtration rate (eGFR) has led to the development of a new race-independent equation (Chronic Kidney Disease Epidemiology Collaboration, CKD-EPI_2021). Previously, some institutions have already modified the early version of the CKD-EPI or Modification of Diet in Renal Disease (MDRD) equations by removing the race factors (CKD-EPI_2009_non-Black (NB), MDRD_NB) for Black populations although this approach remains controversial.

Methods
In this study, the CKD-EPI_2009_NB, MDRD_NB, and European Kidney Function Consortium (EKFC) equations were compared directly with the CKD-EPI_2021 equation in eGFR calculation, chronic kidney disease (CKD) diagnosis, and staging in a local population.

Results
These 3 previous methods underestimated eGFR compared to CKD-EPI_2021 for eGFR &lt; 90 mL/min/1.73 m2 but overestimated eGFR at the high end (&gt;120 mL/min/1.73 m2). Around the CKD diagnosis cutoff (60 mL/min/1.73 m2), both MDRD_NB and EFKC equations resulted in an increase in CKD cases compared to CKD-EPI_2021. CKD-EPI_2009_NB demonstrated a similar trend although the difference was not statistically significant. In a population with low eGFR (&lt;60 mL/min/1.73 m2), the EKFC equation showed a CKD staging pattern significantly different from that by CKD-EPI_2021, but all 3 previous methods resulted in a similar number of end-stage renal failure cases. In general, the EKFC equation demonstrated a weaker agreement in eGFR calculation and concordance in classification with the CKD-EPI_2021 equation than MDRD_NB and CKD-EPI_2009_NB.

Conclusions
Our study provides a direct visual comparison to demonstrate the potential clinical impact between 3 previously used race-independent methods and the CKD-EPI_2021 equation and aids the communication with healthcare providers during the implementation of this new equation.
Assembly and co-occurrence patterns of rhizosphere bacterial communities are closely linked to soil fertility during continuous cropping of cut chrysanthemum (Chrysanthemum morifolium Ramat)
Authors: Li Jun , Meng Feng , Jiang Maibo , Zhang Hanjie , Chu Guixin , Tao Rui 
Published: August 2023

Abstract

Aims
Continuous cropping is known to have profound effects on the soil microbial community in different planting systems. However, we lack an understanding of how different years of continuous cropping affects rhizosphere soil bacterial community co-occurrence pattern and assembly processes in the cut chrysanthemum (Chrysanthemum morifolium Ramat.) field.

Methods and results
We collected the soils from cut chrysanthemum rhizospheres with planting for 1 year (PY1) and continuous cropping for 6 years (CY6) and 12 years (CY12). Real-time quantitative PCR and flow cytometry (FCM) techniques were used to test the 16S rRNA gene copy number and bacterial cell count, respectively. The bacterial community structure was analysed by using high-throughput sequencing technology. The CY12 had a significantly decreased soil fertility index and rhizosphere bacterial living cell counts and gene copy numbers compared to CY6 and PY1 (P &lt; 0.05). The rhizosphere bacterial community dissimilarity increased as the continuous cropping years increased. Three main ecological clusters (modules #1, #2, and #3) were observed in the bacterial co-occurrence network across all samples, and only the relative abundance of module #1 (enriched in the CY12) was significantly correlated with soil fertility (P &lt; 0.05). Moreover, the rhizosphere bacterial community assembly was primarily governed by the deterministic process under 12 years of continuous cropping.

Conclusions
Soil fertility decline correlates with ecological network modularization and the deterministic assembly process of the rhizosphere bacterial community of cut chrysanthemum during continuous cropping.
Automated search methods for identifying wrong patient order entry—a scoping review
Authors: Garrod Mathew , Fox Andy , Rutter Paul 
Published: August 2023

Abstract

Objective
To investigate: (1) what automated search methods are used to identify wrong-patient order entry (WPOE), (2) what data are being captured and how they are being used, (3) the causes of WPOE, and (4) how providers identify their own errors.

Materials and Methods
A systematic scoping review of the empirical literature was performed using the databases CINAHL, Embase, and MEDLINE, covering the period from database inception until 2021. Search terms were related to the use of automated searches for WPOE when using an electronic prescribing system. Data were extracted and thematic analysis was performed to identify patterns or themes within the data.

Results
Fifteen papers were included in the review. Several automated search methods were identified, with the retract-and-reorder (RAR) method and the Void Alert Tool (VAT) the most prevalent. Included studies used automated search methods to identify background error rates in isolation, or in the context of an intervention. Risk factors for WPOE were identified, with technological factors and interruptions deemed the biggest risks. Minimal data on how providers identify their own errors were identified.

Discussion
RAR is the most widely used method to identify WPOE, with a good positive predictive value (PPV) of 76.2%. However, it will not currently identify other error types. The VAT is nonspecific for WPOE, with a mean PPV of 78%–93.1%, but the voiding reason accuracy varies considerably.

Conclusion
Automated search methods are powerful tools to identify WPOE that would otherwise go unnoticed. Further research is required around self-identification of errors.
Anatomical segmentectomy versus wedge resection for small (≤2 cm) peripheral non-small cell lung cancer in 80 or more aged elderly patients: a randomized phase III study (JCOG2109, AWESOME)
Authors: Mimae Takahiro , Wakabayashi Masashi , Sano Yusuke , Sekino Yuta , Aokage Keiju , Okada Morihito , Watanabe Shun-ichi , Saji Hisashi ,   the Lung Cancer Surgical Study Group/Japan Clinical Oncology Group
Published: August 2023

Abstract
The standard treatment for small-sized and peripherally located early-stage non-small cell lung cancer is segmentectomy with secured margins. However, in 80 or more aged elderly patients, whether wedge resection will provide a better prognosis than segmentectomy is controversial. The aim of this trial is to confirm the non-inferiority of wedge resection to anatomical segmentectomy in terms of overall survival in these patients, who can tolerate lobectomy, with small-sized (≤2 cm), radiological solid dominant (consolidation-to-tumour ratio &gt;0.5) and peripherally located early-stage non-small cell lung cancer in a randomized phase III trial. The primary endpoint is overall survival. If the non-inferiority of overall survival and the minimal invasiveness of wedge resection are proven, it can be a new standard treatment for such patients. A planned total of 400 patients will be enrolled from 53 institutions in 5 years. This trial has been registered in the Japan Registry of Clinical Trials with code jRCT1030220482 (https://jrct.niph.go.jp/latest-detail/jRCT1030220482).
Nondestructive initial-profile-free 3D elemental mapping in multilayer thin film structures based on EDX and a quadratic programming problem
Authors: Hoshina Yutaka , Kubo Yugo , Nakayama Yojiro 
Published: August 2023

Abstract
We have demonstrated a new data analysis method that enables nondestructive depth profiling of a multilayer thin-film sample from energy-dispersive X-ray spectroscopy (EDX) data without the assumption of initial profiles. This method is based on a quadratic programming problem and allows for three-dimensional elemental mapping in the sample without destroying it, by performing depth profiling for all the pixels in the EDX two-dimensional mapping data. In this paper, first nondestructive depth profiling of two samples with different multilayer structures was performed using the proposed method. The results were compared with those obtained by cross-sectional observation to validate the accuracy and usefulness of the proposed method. Next, an example of the three-dimensional elemental mapping based on the proposed method was demonstrated. This method allows us to nondestructively obtain three-dimensional elemental distribution within a sample over a wide area on the order of mm, which is impossible to obtain using other analytical methods. The way to determine the hyperparameters, which significantly affects the calculation results, is fully described in this paper.
Refractory chylothorax after severe vomiting and coughing in a 4-year-old child
Authors: De Pauw Vincent , Daelemans Siel , Depoorter Leontien , Brussaard Carola , Smets Dirk 
Published: August 2023

Abstract
Chylothorax is the accumulation of lymphatic fluid in the pleural space. It is a rare condition with potentially life-threatening disorders. In children, the etiology of chylothorax can be mainly attributed to idiopathic factors, congenital, miscellaneous, trauma and malignancies. Conservative treatments can solve most chylothorax, but refractory chylothorax can be challenging to manage. We herein present the case of a 4-year-old girl with no previous medical history who was admitted to our institution after severe vomiting and right chylothorax. The etiological assessment could not identify specific causes. Initial treatment was conservative but after 14 days, the patient showed no improvement. An exploratory thoracoscopy using indocyanine green showed no active leaks. Pleurodesis was performed and, later on, ligation of the ductus thoracicus. Hereafter, the patient progressed favorably. Even though conservative treatments of chylothorax show a high success rate, the efficacy of additional therapies and the benefits between surgical procedures need further investigation.
A fuzzy structure processing mechanism for graph grammar
Authors: Liu Yufeng , Yang Fan , Liu Jian , Li Song 
Published: August 2023

Abstract
A strict graph-matching mechanism brings normativeness to graph grammar but leads to graph grammar insufficiency when processing fuzzy grammatical structures. To address this issue, the current paper proposes an improved formal framework for graph grammar that enables it to effectively specify the ambiguity of graph models while maintaining normativeness and intuition. First, the improved framework defines the connection probability for edges and classifies the edges based on the connection probability, which is used as the quantitative and qualitative description of the graph grammar structure’s ambiguity. Second, the concepts of credibility threshold, credible subgraphs and candidate subgraphs are defined, and the constraints on the redex are adjusted to increase the fault tolerance of the graph-matching process. Finally, the grammatical operation is redesigned, with a matching weight defined for each redex based on the connection probability and the credibility threshold, thereby providing a theoretical basis and practical guidance for the selection of multiple redexes.
Perspective on receptor-associated immune response to Candida albicans single and mixed infections: Implications for therapeutics in oropharyngeal candidiasis
Authors: Yang Liu , Cheng Ting , Shao Jing 
Published: August 2023

Abstract
Oropharyngeal candidiasis (OPC), commonly known as ‘thrush’, is an oral infection that usually dismantles oral mucosal integrity and malfunctions local innate and adaptive immunities in compromised individuals. The major pathogen responsible for the occurrence and progression of OPC is the dimorphic opportunistic commensal Candida albicans. However, the incidence induced by non-albicans Candida species including C. glabrata, C. tropicalis, C. dubliniensis, C. parapsilosis, and C. krusei are increasing in company with several oral bacteria, such as Streptococcus mutans, S. gordonii, S. epidermidis, and S. aureus. In this review, the microbiological and infection features of C. albicans and its co-contributors in the pathogenesis of OPC are outlined. Since the invasion and concomitant immune response lie firstly on the recognition of oral pathogens through diverse cellular surface receptors, we subsequently emphasize the roles of epidermal growth factor receptor, ephrin-type receptor 2, human epidermal growth factor receptor 2, and aryl hydrocarbon receptor located on oral epithelial cells to delineate the underlying mechanism by which host immune recognition to oral pathogens is mediated. Based on these observations, the therapeutic approaches to OPC comprising conventional and non-conventional antifungal agents, fungal vaccines, cytokine and antibody therapies, and antimicrobial peptide therapy are finally overviewed. In the face of newly emerging life-threatening microbes (C. auris and SARS-CoV-2), risks (biofilm formation and interconnected translocation among diverse organs), and complicated clinical settings (HIV and oropharyngeal cancer), the research on OPC is still a challenging task.