bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association between the
ABCC11
gene polymorphism-determined earwax properties and external auditory canal microbiota in healthy adults
Authors: Amari Yasunobu , Hosonuma Masahiro , Mizukami Takuya , Isobe Junya , Azetsu Yuki , Funayama Eiji , Maruyama Yuki , Tsurui Toshiaki , Tajima Kohei , Sasaki Aya , Yamazaki Yoshitaka , Nakano Ryota , Sano Yutaka , Ishida Atsushi , Nakanishi Tatsuya , Mochizuki Seiji , Yoshizawa Yuri , Kumagai Sumito , Yasuhara Sakiko , Ryu Kakei , Oguchi Tatsunori , Kuramasu Atsuo , Yoshimura Kiyoshi , Sambe Takehiko , Kobayashi Sei , Uchida Naoki 
Published: January 2025

ABSTRACT

The concept of genome–microbiome interactions, in which the microenvironment determined by host genetic polymorphisms regulates the local microbiota, is important in the pathogenesis of human disease. In otolaryngology, the resident bacterial microbiota is reportedly altered in non-infectious ear diseases, such as otitis media pearls and exudative otitis media. We hypothesized that a single-nucleotide polymorphism in the ATP-binding cassette sub-family C member 11 (
ABCC11
) gene, which determines earwax properties, regulates the ear canal microbiota. We analyzed
ABCC11
gene polymorphisms and ear canal microbiota in healthy individuals to understand the relationship between genome–microbiome interactions in the ear canal. The study included 21 subjects who were divided into two groups: 538GA (9) and 538AA (12).
Staphylococcus auricularis
and
Corynebacterium
spp. were observed in the 538GA group, whereas
Methylocella
spp. was observed in the 538AA group. PICRUSt analysis revealed significant enrichment of certain pathways, such as superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation, chlorosalicylate degradation, mycothiol biosynthesis, and enterobactin biosynthesis in the GA group, whereas allantoin degradation IV (anaerobic), nitrifier denitrification, starch degradation III, L-valine degradation I, and nicotinate degradation I were significantly enriched in the AA group. The
ABCC11
gene polymorphism regulates the composition of the ear canal microbiota and its metabolic pathways. This study revealed a genome–microbiome interaction within the resident microbiota of the external auditory canal that may help to elucidate the pathogenesis of ear diseases and develop novel therapies.

IMPORTANCE

The
ABCC11
gene polymorphism, which determines earwax characteristics, regulates the composition of the ear canal microbiota and its metabolic pathways. We determined the presence of genome–microbiome interactions in the resident microbiota of the ear canal. Future studies should focus on
ABCC11
gene polymorphisms to elucidate the pathogenesis of ear diseases and develop therapeutic methods.
Molecular identification and antibiotic clearance of
Mycoplasma arginini
and
Mycoplasma orale
from cell cultures infected with
Rickettsia
or
Ehrlichia
species
Authors: Allerdice Michelle E. J. , Shooter Savannah L. , Galletti Maria F. B. M. , Hecht Joy A. , Karpathy Sandor E. , Paddock Christopher D. 
Published: January 2025

ABSTRACT

Mycoplasma (Class: Mollicutes) contamination in cell cultures is a universal concern for research laboratories. Some estimates report contamination in up to 35% of continuous cell lines. Various commercial antibiotic treatments can successfully decontaminate clean cell lines
in vitro
; however,
in vitro
decontamination of bacterial cultures remains challenging. Intracellular bacteria like those in the genera
Rickettsia
and
Ehrlichia
require cell culture for primary isolation and propagation and are thus vulnerable to contamination with mycoplasmas. Some analyses have reported successful antibiotic clearance of contaminating mycoplasmas in
Rickettsia
cultures; however, many of these studies do not identify the contaminating mycoplasma species and often include only a few isolates. To our knowledge, there are no published studies reporting decontamination of mycoplasmas from
Ehrlichia
cultures. In this study, we developed a specific multiplex assay to identify two of the most common mycoplasma culture contaminants,
Mycoplasma arginini
and
Mycoplasma orale
, in cell cultures infected with
Rickettsia
or
Ehrlichia
species. We further describe the successful
in vitro
decontamination of
M. arginini
,
M. orale,
and co-contaminations with both mycoplasmas from multiple
Rickettsia
and
Ehrlichia
cultures using daptomycin and clindamycin.

IMPORTANCE

Mycoplasma contamination is a frequent problem in bacterial cell culture. These prolific organisms thrive in the extracellular environment
in vitro
and can persist in cell lines indefinitely without treatment. Historically, mycoplasma-contaminated
Rickettsia
cultures were cleared of contaminants by inoculating laboratory mice and re-isolating mycoplasma-free
Rickettsia
from brain endothelial cells. However, this method requires the sacrifice of live animals and is not always effective. Mycoplasma clearance via mouse inoculation requires a patent infection of murine central nervous system endothelial cells, which may not occur with some mildly pathogenic or nonpathogenic rickettsial species.
In vitro
antibiotic treatment represents an alternate method to eliminate contaminating mycoplasmas from rickettsial cultures. This method requires minimal adjustment of laboratories that already maintain rickettsial cultures and is not dependent on the use of laboratory animals. As such, the comprehensive strategy for
Mycoplasma arginini
and
Mycoplasma orale
elimination presented here can improve laboratory efficiency for
in vitro
research with intracellular bacteria.
Enhanced bacteriostatic effects of phage vB_C4 and cell wall-targeting antibiotic combinations against drug-resistant
Aeromonas veronii
Authors: Cao Xin , Tang Yanqiong , Lu ZhenZhang , Ma Xiang , Li Hong , Chi Xue , Li Juanjuan , Liu Zhu 
Published: January 2025

ABSTRACT

Aeromonas veronii
is a vital zoonotic pathogen known for its extensive drug resistance and ability to form biofilms, which contribute to its antibiotic resistance. In this study, the phage vB_C4, specifically targeting
A. veronii
, was isolated and subjected to bioinformatic analysis and bacteriostatic activity assays. The combination of phage vB_C4 with antibiotics such as cephalothin and cefoxitin, which target the bacterial cell wall, resulted in a significantly enhanced bacteriostatic effect compared to either the phage or antibiotics alone. Furthermore, the phage dosage was critical in optimizing the antimicrobial effect when used in conjunction with antibiotics. This combined treatment exhibited a more distinct effect in removing mature biofilms and inhibiting biofilm formation, leading to a considerable decrease in bacterial density within the biofilm. Overall, the synergistic use of phage and antibiotics offers a novel attitude for treating pathogenic bacteria and holds significant potential in preventing the emergence of drug-resistant strains.

IMPORTANCE
The combined application of phages and antibiotics not only effectively inhibits the emergence of phage-resistant bacteria but also reduces the required effective concentration of antibiotics. Additionally, this combination therapy demonstrates significant therapeutic effects on clinical infections mediated by biofilms. Consequently, this study establishes a basis for evaluating the parameters essential for utilizing phage-antibiotic combination therapy in the treatment of biofilm-associated infections, thereby offering a novel selection for the clinical management of multidrug-resistant bacterial infections.
CRISPR/Cas9-mediated genomic insertion of functional genes into
Lactiplantibacillus plantarum
WCFS1
Authors: Wiull Kamilla , Haugen Lisa K. , Eijsink Vincent G. H. , Mathiesen Geir 
Published: January 2025

ABSTRACT

Lactiplantibacillus plantarum,
a natural inhabitant of the human body, is a promising candidate vehicle for vaccine delivery. An obstacle in developing bacterial delivery vehicles is generating a production strain that lacks antibiotic resistance genes and contains minimal foreign DNA. To deal with this obstacle, we have constructed a finetuned, inducible two-plasmid CRISPR/Cas9-system for chromosomal gene insertion in
L. plantarum
. The knock-in plasmid was designed with a cassette-like structure to simplify the insertion of target DNA and streamline the CRISPR/Cas9 genome editing, bringing it one step closer to becoming a routine procedure. We demonstrate that the system enables efficient insertion of expression cassettes for both inducible and constitutive production of a fluorescent reporter protein, mCherry, and for inducible production of the receptor-binding domain (RBD) of the SARS-CoV-2 virus. Two variants of RBD were successfully expressed, one directed to the cytoplasm and one directed to the cell surface. All the knock-in strains produced the target protein, although with lower yields than strains with plasmid-encoded expression.

IMPORTANCE

Genetic engineering of lactic acid bacteria, such as
Lactiplantibacillus plantarum,
has proven to be difficult. This study presents an inducible two-plasmid CRISPR/Cas9-system for inserting genes into the chromosome of
Lactiplantibacillus plantarum
. Our system successfully knock-in four expression cassettes varying in length from ~800–1,300 bp with high efficiency and insert an expression cassette encoding a SARS-CoV-2 antigen receptor-binding domain (RBD) with an anchor mediating surface display, which has not been achieved previously using CRISPR/Cas9. We demonstrate the production of the insertion genes. Importantly, the plasmid carrying the SgRNA, Cas9, and homology-directed repair template is designed for easy component exchange. These plasmids represent valuable contributions to the field as they could facilitate rapid CRISPR/Cas9 engineering of
L. plantarum
strains.
Glutathione reductase plays a role in the metabolism of methylmercury degradation in
Rhodotorula mucilaginosa
Authors: Guo Yi , Deng Wenlong , Mo Qigui , Yu You , Zhang Zhenwang , Wei Mingjie , Tang Ruiling , Lu Surui , Su Yanting 
Published: January 2025

ABSTRACT

Mercury pollution is a kind of heavy metal pollution with great harm and strong toxicity which exists worldwide. Some microorganisms can convert highly toxic methylmercury into inorganic mercury compounds with significantly reduced toxicity. This is an effective means of methylmercury pollution remediation. As a safe microorganism with great potential in the remediation of heavy metal pollution,
Rhodotorula mucilaginosa
has not been studied in the remediation of methylmercury. Here, a
R. mucilaginosa
strain Rm4 with high methylmercury resistance was obtained by wild-strain screening. Its minimal inhibitory concentration and minimum lethal concentration reached 3 and 6 mg/L, respectively. At the same time, Rm4 can also degrade methylmercury. Unlike the traditional microbial methylmercury degradation pathways,
R. mucilaginosa
’s genome does not encode the organomercury lyase gene MerB. However, transcriptomic analysis revealed that the glutathione reductase of
R. mucilaginosa
responds to the methylmercury degradation process. Structural domain analysis and molecular docking experiments suggest that the glutathione reductase of
R. mucilaginosa
has the potential to directly or indirectly participate in methylmercury degradation metabolism. Metabolic indicator tests of engineered strains overexpressing the glutathione reductase encoding gene also support this notion.

IMPORTANCE

The remediation of methylmercury pollution is crucial for environmental health. The ability of
Rhodotorula mucilaginosa
to resist and degrade methylmercury offers a new avenue for bioremediation efforts. Understanding the metabolic pathways involved, particularly the role of glutathione reductase, enhances our knowledge of how
Rhodotorula mucilaginosa
responds to methylmercury and opens up new possibilities for future research in bioremediation strategies.
Macrolide resistance due to
erm
(55)
Authors: Alexander David C. , Farquhar Tayah , Adams Joshua M. E. , Suchan Danae M. , Workman Sean D. , Wallace Richard J. , Brown-Elliott Barbara A. , El-Halfawy Omar M. , Cameron Andrew D. S. 
Published: January 2025

ABSTRACT

Antimicrobial resistance (AMR) is a global threat. The identification and
characterization of novel resistance genes is integral to AMR surveillance.
The
erm
(55) gene was originally identified through whole
genome sequencing of macrolide-resistant strains of
Mycobacterium
chelonae
. The gene was annotated as a ribosomal
methyltransferase, but its role as a determinant of macrolide resistance was
not formally demonstrated. Three
erm
(55) alleles have now
been documented. The plasmid-borne
erm
(55)
P
, the
transposon-associated
erm
(55)
T
, and the
chromosomal encoded
erm
(55)
C
exhibit ≈82%
amino acid sequence identity. Here, we confirm that, when expressed from
plasmids in a macrolide-susceptible strain of
Escherichia
coli
, all three
erm
(55) variants confer
resistance to azithromycin and clarithromycin.

IMPORTANCE

Macrolide antibiotics are often the only oral treatment option for infections
with rapidly growing mycobacteria such as
Mycobacterium
abscessus
and
Mycobacterium chelonae
. We
previously identified three variants of a newly predicted macrolide
resistance gene,
erm
(55), in
M. chelonae
,
including the first case of a plasmid-mediated macrolide resistance in
mycobacteria. The present study provides experimental evidence that the
three
erm
(55) variants confer macrolide resistance and that
each variant is unique in the degree to which it reduces susceptibility to
clinically relevant macrolides.
Supplying standardized ileal digestible lysine via soybean meal below estimated requirements for late gestating gilts does not negatively affect mammary development
Authors: Gillies C.R. , Farmer C. , Huber L. 
Published: January 2025

Forty-eight Yorkshire × Landrace gilts were used to determine whether supplying lysine via soybean meal below estimated requirements influences mammary development in late gestation. Gilts were assigned one of three isocaloric (2505 kcal/kg net energy) diets on gestation day 90: (1) control (CON; 18.38% crude protein (CP); 18.2 g/day standardized ileal digestible (SID) Lys, being near NRC (2012) estimated requirements; n = 16), or diets that provided SID Lys below estimated requirements with Lys supplied primarily by soybean meal: SBM1 (14.69% CP; 12.4 g SID Lys/day; n = 16) or SBM2 (17.81% CP; 14.6 g SID Lys/day; n = 16). Mammary development was assessed on gestation day 110. Gilt body weight and backfat depth gain between gestation days 90 and 110 were not influenced by dietary treatment ( P > 0.10). Moreover, mammary parenchymal and extraparenchymal tissue masses, as well as protein and fat contents and concentrations of DNA and RNA in parenchymal tissue were not influenced by dietary treatment ( P > 0.10). Therefore, providing Lys up to 34% below estimated requirements via soybean meal in late gestation had no immediate detrimental effect on mammary development.
Enhanced Benefit of STA‐MCA Bypass Surgery in Chronic Terminal Internal Carotid and/or Middle Cerebral Artery Occlusion Patients With Impaired Collateral Circulation: Introducing a Novel Assessment Approach for Collateral Compensation
Authors: Qiu Cheng , Zhang Yanping , Yu Zhiqiang , Xu Yonghui , Huang Yongjiang , Huang Tianci , Ma Jun , Zhao Jinbing 
Published: January 2025

Background: Ischemic stroke is one of the major emergency diseases leading to death and disability worldwide, characterized by its acute onset and the urgent need for prompt medical intervention to reduce mortality and long‐term disability. Chronic terminal internal carotid artery and/or middle cerebral artery occlusion (CTI/MCAO) is an important subtype of intracranial artery occlusive disease. The superficial temporal artery‐to‐MCA (STA‐MCA) bypass has been proposed to improve cerebral blood flow (CBF) and cerebrovascular reserve (CVR), potentially enhancing neurological outcomes. However, its safety and efficacy in CTI/MCAO patients remain controversial.Methods: A total of 107 CTI/MCAO patients from Nanjing Brain Hospital, enrolled between July 2019 and June 2022, were divided into surgical and medical treatment groups. Cerebral perfusion and collateral formation were evaluated using pseudocontinuous arterial spin labeling (pCASL) and digital subtraction angiography (DSA). Modified Rankin scale (mRS) score and complication rates were compared between the two groups. In addition, correlations between Matsushima grades, early‐arriving flow proportion (EFP), and lesion‐side cerebrovascular (LCBV) scores were analyzed.Results: The surgical group showed significantly lower mRS scores than the medical group (p = 0.018), with no significant differences in complication rates at the 6‐month follow‐up (p = 0.861). CBF differed significantly among affected MCA segments (p < 0.001), particularly in the insular and opercular regions (M2‐M3) (p = 0.006). Matsushima grades in unilateral CTI/MCAO patients were negatively correlated with preoperative LCBV scores (γs = −0.468, p = 0.005) and EFP (γs = −0.648, p = 0.007). EFP demonstrated high accuracy in predicting LCBV scores in CTI/MCAO patients (AUC = 0.902, p = 0.004).Conclusion: STA‐MCA bypass surgery improved neurological outcomes in CTI/MCAO patients, particularly those with poor preoperative collateral compensation. EFP may serve as a reliable, noninvasive tool for assessing collateral circulation status in this population.
Qualitative and Quantitative Evaluation of the Image Quality of MDCT Multiphasic Liver Scans in HCC Patients
Authors: El-Sayed Mohamed Zakaria , Rawashdeh Mohammad , Hassan Hend Galal Eldeen Mohamed Ali , El Safwany Mohamed M. , Islam I. E.  , Khedr Yasser I. , Soula Moustafa A. , Ali Magdi A. 
Published: January 2025

Background: The quality of CT images obtained from hepatocellular carcinoma (HCC) patients is complex, affecting diagnostic accuracy, precision, and radiation dose assessment due to increased exposure risks.Objectives: The study evaluated image quality qualitatively and quantitatively by comparing quality levels with an effective radiation dose to ensure acceptable quality accuracy.Materials and Methods: This study retrospectively reviewed 100 known HCC patients (Li‐RADS‐5) who underwent multidetector computed tomography (MDCT) multiphasic scans for follow‐up of their health condition between January and October 2023. The evaluation involved quantitative and qualitative analyses of parameters such as SD, SNR, and CNR, as well as a qualitative assessment by two radiology consultants. The outcomes were compared, and the effective dose was calculated and compared with both quantitative and qualitative assessments of image quality.Results: ROC curve analysis revealed significant differences in CT image quality, with high to moderate specificity and sensitivity across all the quantitative parameters. However, multivariate examination revealed decreasing importance levels, except for CNR (B, 0.203; p = 0.001) and SD BG (B, 0.330; p = 0.002), which increased in B. The CNR and SD BG remained independent variables for CT image quality prediction, but no statistically significant relationship was found between the effective dose and image quality, either quantitatively or qualitatively.Conclusion: This study underscores the vital role of both quantitative and qualitative assessments of CT images in evaluating their quality for patients with HCC and highlights the predictive importance of CNR, SNR, and SD. These findings emphasize the value of these devices in assessing and predicting outcomes to minimize the effective dose.
Evaluation of Emerging Antimicrobials Resistance in Nosocomial Infections Caused by E. coli: The Comparison Results of Observed Cases and Compartmental Model
Authors: Eshrati Babak , Karimzadeh-Soureshjani Elaheh , Nasehi Mahshid , Janani Leila , Baradaran Hamid Reza , Bitaraf Saeid , Simab Pouria Ahmadi , Mobarak Sara , Kalkhajeh Sasan Ghorbani , Kogani Mohammad 
Published: January 2025

Background: In recent years, the global rise of antibiotic‐resistant Escherichia coli (E. coli) has become a significant threat to public health. This study aimed to identify and track outbreaks of antibiotic resistance, specifically among the antibiotics used to treat nosocomial E. coli infections.Materials and Methods: This hospital‐based study utilized data from a nosocomial infection surveillance system to investigate reported cases of antibiotic resistance. The study analyzed the results of 12,954 antibiogram tests conducted across 57 hospitals in 31 provinces of Iran. The data was divided into two periods: the first and second halves of 2017. Before developing a predictive model for resistant E. coli cases, the model’s validity was tested using the first half of the year’s data. The predicted cases were then compared to the actual observed cases in 2017, with a statistically significant difference indicating an outbreak.Findings: The study found that, in 2017, hospitals in Iran experienced an outbreak of E. coli resistant to ampicillin and ceftazidime. This resistance was more prevalent than expected, highlighting the emergence of these drugs as major contributors to nosocomial E. coli infections.Conclusion: This study demonstrated the utility of the compartmental model in forecasting outbreaks of antibiotic‐resistant E. coli. It provides a framework for investigating similar outbreaks in the future, using diverse data sources and methodologies.
Association Between Glycemic Control and Complications With Concentration of Urinary Exfoliated Proximal Tubule Kidney Cells in People With Diabetes Mellitus
Authors: Wu Henry H. L. , Bhagavath Venkatesha , Nguyen Long The , Chinnadurai Rajkumar , Goldys Ewa M. , Pollock Carol A. , Saad Sonia 
Published: January 2025

Background: Emerging evidence suggests cell exfoliation could be operating under the control of cell metabolism. It is unclear if there are associations between the concentration of exfoliated kidney proximal tubule cells (PTCs) in urine with glycemic control and complications. Our study is aimed at exploring this.Methods: Urine samples were collected from 122 adult study participants and stored at −80°C. Exfoliated PTCs were extracted from thawed urine using a validated specific immunomagnetic separation method based on anti‐CD13 and anti‐SGLT‐2 antibodies. The number of PTCs was assessed using brightfield microscopy. Study participants were grouped into those with no diabetes mellitus (DM) and those with DM. Individuals with DM were further subgrouped into those with and without retinopathy. Adjusted Poisson regression analysis was conducted for the DM cohort, investigating associations between demographic, clinical, and biochemical parameters with mean urinary exfoliated PTCs.Results: The adjusted Poisson regression analysis noted sex to have a significant association with mean number of urinary exfoliated PTCs, with a lower incidence rate in males compared to females (incidence rate ratio (IRR) 0.56, 95% CI 0.35–0.89, p = 0.014). Each 1% increase in glycated haemoglobin (HbA1c) was associated with an increase of 1.03 times in mean exfoliated PTCs (IRR 1.03, 95% CI 1.01–1.04, p = 0.007), and DM patients with retinopathy had an increase of 1.68 times in mean exfoliated PTCs compared to those without retinopathy (IRR 1.68, 95% CI 1.07–2.62, p = 0.024). No significant associations were observed with albuminuria or estimated glomerular filtration rate (eGFR).Conclusions: Our results indicate increased shedding of PTCs into the urinary tract in patients with poorer glycemic control, particularly those with diabetic retinopathy and in females.