bluuebunny/crossref_metadata_2025 huggingface dataset:
Enterohemorrhagic
Escherichia coli
(EHEC) disrupts intestinal barrier integrity in translational canine stem cell-derived monolayers
Authors: Nagao Itsuma , Kawasaki Minae , Goyama Takashi , Kim Hyun Jung , Call Douglas R. , Ambrosini Yoko M.
Published: August 2024

This study addresses the gap in translatable
in vitro
models for investigating Enterohemorrhagic
E. coli
(EHEC) infections, particularly relevant to both canine and human health. EHEC is known to induce acute colitis in dogs, leading to symptoms like hemorrhagic diarrhea and hemolytic uremic syndrome, similar to those observed in humans. However, understanding the pathophysiology and developing treatment strategies have been challenging due to the lack of effective models that replicate the clinical disease caused by EHEC in both species. Our approach involved the development of colonoid-derived monolayers using intestinal tissues from healthy, client-owned dogs. These monolayers were exposed to EHEC, and the impact of EHEC was assessed through several techniques, including trans-epithelial electrical resistance (TEER) measurement, immunofluorescence staining for junction proteins and mucus, and scanning electron microscopy for morphological analysis. Modified culture with saline, which was intended to prevent bacterial overgrowth, maintained barrier integrity and cell differentiation. EHEC infection led to significant decreases in TEER and ZO-1 expression, but not in E-cadherin levels or mucus production. In addition, EHEC elicited a notable increase in tumor necrosis factor-alpha production, highlighting its distinct impact on canine intestinal epithelial cells compared to non-pathogenic
E. coli
. These findings closely replicate
in vivo
observations in dogs and humans with EHEC enteropathy, validating the canine colonoid-derived monolayer system as a translational model to study host-pathogen interactions in EHEC and potentially other clinically significant enteric pathogens.

IMPORTANCE

This study develops a new model to better understand Enterohemorrhagic
E. coli
(EHEC) infections, a serious bacterial disease affecting both dogs and humans, characterized by symptoms such as hemorrhagic diarrhea and hemolytic uremic syndrome. Traditional research models have fallen short of mimicking how this disease manifests in patients. Our research used intestinal tissues from healthy dogs to create layers of cells, known as colonoid-derived monolayers, which we then exposed to EHEC. We assessed the damage caused by the bacteria using several techniques, observing significant changes similar to those seen in actual cases of the disease. The model proved effective in replicating the interaction between the host and the pathogen, marking an important step toward understanding EHEC’s effects and developing treatments. This canine colonoid-derived monolayer system not only bridges a crucial gap in current research but also offers a promising platform for studying other enteric pathogens affecting both canine and human health.
Performance of common primary and chromogenic culture media for MALDI-TOF MS identification of clinically relevant yeasts
Authors: Lévesque Simon , Brown Nathalie , Dufresne Philippe J. , Allard Catherine
Published: August 2024

Timely and accurate identification of yeasts is essential for adequate treatment, considering the increase in antifungal resistance of some species, particularly for
C. auris
. Current matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) manufacturer’s protocol for identification of yeasts requires 24- to 72-h cultivation on Sabouraud dextrose media (SAB), but not some of the mainstay primary culture media used in mycology such as inhibitory mold agar (IMA), Mycosel, CHROMagar Candida Plus, and CHROMagar Candida. As culture media can influence MALDI-TOF MS identification results, this study evaluated the accuracy and performance of identification of clinically relevant yeasts on these first-line media using the VITEK-MS MALDI-TOF MS system.

IMPORTANCE

In this study, a panel of 140 strains (21 species) was used to assess the performance of the selected media. Although not in the manufacturer’s list of accepted media, IMA and chromogenic media are suitable for the identification of yeasts on the VITEK-MS systems. CHROMagar Candida Plus allowed the identification of 135/140 isolates tested after 24-h incubation similar to SAB reference media (137/140). Yeast isolates that grew on Mycosel selective media were also reliably identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. VITEK-MS system with IVD database V3.2 correctly identified
C. auris
strains to the species level on CHROMagar Candida Plus alleviating the need for subcultivation and reduced turnaround time (24–72 h) to identification for patient screening.
Emergence of a novel sequence type carbapenem-resistant hypervirulent
Klebsiella pneumoniae
ST6417 harboring
bla
NDM-5
on the lncX3 plasmid
Authors: Liu Junnian , Yuan Sue , Xuan Luhan , Sun Yu , Zhang Xinyu , Qiao Lu , Du Xuefei
Published: August 2024

Carbapenem-resistant hypervirulent
Klebsiella pneumoniae
(CR-hvKP) is a significant pathogen causing major public health problems worldwide. This study characterized a novel sequence type 6417 (ST6471) CR-hvKP strain recovered from the blood of a male patient with septicemia. Strain CR2021 is not susceptible to carbapenems, cephalosporin, sulfonamides, quinolones, or levofloxacin and is susceptible to amikacin and tigecycline. Molecular typing indicated that ST6417 is derived from the most dominant hypervirulent
K. pneumoniae
(hvKP) clone in China, ST23, with a single-locus variation in
tonB
. The genomic characterization of CR2021, which contains three plasmids, was performed through whole-genome sequencing. The plasmid pCR2021_IncFII contains 12 antibiotic resistance genes [
bla
CTX-M-3
,
bla
TEM-1B
,
bla
DHA-1
,
aac (3)-Ild
,
aadA16
,
sul1
,
sul2
,
qnrB4
,
ARR-3
,
dfrA27
,
qacE
,
merACDE
], all of which are associated with genetic elements. The plasmid pCR2021_IncFIB carries crucial virulence-related genes, while the plasmid pCR2021_IncX3 only harbors the
bla
NDM-5
resistance gene and exhibits 99% similarity with two other
bla
NDM-5
-carrying IncX3 plasmids (pSHX180-NDM5, pNDM-K725), with coverage of 87% and 100%, respectively. The
bla
NDM-5
genetic region contains an additional IS26-Tn3 genetic module. Serum killing and anti-human neutrophil phagocytosis tests indicated that CR2021 exhibits high virulence, which was further confirmed in a
Galleria mellonella
larvae infection model. CR-hvKP is becoming more prevalent in China; however, the majority have evolved from the multidrug resistance clone ST11 and its variants by acquiring virulence factors. Conversely, CR-hvKP derived from hvKP, such as the clone ST23, remains relatively rare. Therefore, the discovery of ST6417 underscores the need for further research into the genetic characteristics and evolution of bacteria.

IMPORTANCE

ST11 and its variants, which often exhibit drug resistance, represent popular clones of carbapenem-resistant hypervirulent
Klebsiella pneumoniae
(CR-hvKP) in China, often leading to high morbidity and mortality rates owing to their high virulence and robust drug resistance. Conversely, CR-hvKP, originating from the high-virulence sequence type ST23, remains rarely reported. In this study, we identified a novel ST6417 CR-hvKP strain derived from ST23, carrying
bla
NDM-5
on an IncX3 plasmid conferring resistance to carbapenems. In addition, we elucidate its virulence, resistance to drugs, and genetic characteristics. The discovery of ST6417 highlights the diverse pathways in the evolution of CR-hvKP, warranting increased attention.
In vitro
small molecule screening to inform novel candidates for use in fluconazole combination therapy
in vivo
against
Coccidioides
Authors: Mead Heather L. , Valentine Michael , Yin Holly , Thompson III George R. , Keim Paul , Engelthaler David M. , Barker Bridget M.
Published: August 2024

Identifying improved treatments for severe and refractory coccidioidomycosis (Valley fever) is needed. This endemic fungal disease is common in North and South America, and cases have increased substantially over the last 30 years. The current standard of care, oral daily fluconazole, often fails to completely eradicate
Coccidioides
infection; however, the high cost of identifying new compounds effective in treating Valley fever is a barrier to improving treatment. Therefore, repurposing existing pharmaceutical agents in combination with fluconazole therapy is an attractive option. We screened the Library of Pharmacologically Active Compounds (LOPAC) small molecule library for compounds that inhibited fungal growth
in vitro
and determined IC
50
values for a subset of compounds. Based on these findings, we tested a small subset of these agents to validate the screen, as well as to test the performance of fluconazole in a combination therapy approach, as compared with fluconazole alone, in a murine model. We observed that combination therapy of tamoxifen:fluconazole and sertraline:fluconazole significantly reduced the burden of live fungus in the lung compared with fluconazole alone, and we observed reduced or nonexistent dissemination. These results suggest that tamoxifen and sertraline may be repurposed as adjunctive agents in the treatment of this important fungal disease.

IMPORTANCE

Developing new drugs, especially for regional orphan diseases, such as Valley Fever, is a slow and costly endeavor. However, there is a wealth of FDA-approved drugs available for repurposing, offering a more economical and expedited approach to improve treatment. Those existing compounds with antifungal properties can become novel therapies with relative ease: a considerable advantage for patients in need of alternative treatment. Despite the scope of remaining tasks, our comprehensive screening of potential candidates has revealed promising combinations for further exploration. This effort outlines a practical pipeline for Valley fever drug screening and identifies viable drug combinations that could impact patients more rapidly than single drug development pathways.
Exploring antimicrobial interactions between metal ions and quaternary ammonium compounds toward synergistic metallo-antimicrobial formulations
Authors: Lekhan Andrii , Turner Raymond J.
Published: August 2024

Multi-target antimicrobial agents are considered a viable alternative to target-specific antibiotics, resistance to which emerged as a global threat. Used centuries before the discovery of conventional antibiotics, metal(loid)-based antimicrobials (MBAs), which target multiple biomolecules within the bacterial cell, are regaining research interest. However, there is a significant limiting factor—the balance between cost and efficiency. In this article, we utilize a checkerboard assay approach to explore antimicrobial combinations of MBAs with commonly used quaternary ammonium compound (QAC) antiseptics in order to discover novel combinations with more pronounced antimicrobial properties than would be expected from a simple sum of antimicrobial effects of initial components. This phenomenon, called synergy, was herein demonstrated for several mixtures of Al3+with cetyltrimethylammonium bromide (CTAB) and TeO32- with benzalkonium chloride (BAC) and didecyldimethylammonium bromide (DDAB) against planktonic and biofilm growth of
Pseudomonas aeruginosa
ATCC27853. Biofilm growth of
Escherichia coli
ATCC25922 was synergistically inhibited by the Cu2 +and benzalkonium chloride (BAC) mixture. Multiple additive mixtures were identified for both organisms. The current study observed unexpected species and growth state specificities for the synergistic combinations. The benefit of synergistic mixtures will be captured in economy/efficiency optimization for antimicrobial applications in which MBAs and QACs are presently used.

IMPORTANCE

We are entering the antimicrobial resistance era (AMR), where resistance to antibiotics is becoming more and more prevalent. In order to address this issue, various approaches are being explored. In this article, we explore for synergy between two very different antimicrobials, the antiseptic class of quaternary ammonium compounds and antimicrobial metals. These two antimicrobials have very different actions. Considering a OneHealth approach to the problem, finding synergistic mixtures allows for greater efficacy at lower concentrations, which would also address antimicrobial pollution issues.
Respiratory virus disease and outcomes at a large academic medical center in the United States: a retrospective observational study of the early 2023/2024 respiratory viral season
Authors: Mostafa Heba H. , Fall Amary , Norton Julie M. , Sachithanandham Jaiprasath , Yunker Madeline , Abdullah Omar , Hanlon Ann , Gluck Linda , Morris C. Paul , Pekosz Andrew , Klein Eili Y.
Published: August 2024

Respiratory disease, attributed to influenza, respiratory syncytial virus (RSV), and SARS-CoV-2, was reported nationally during the 2023/2024 respiratory viral season. The emergence of novel SARS-CoV-2 variants was considered a significant factor contributing to the rise in COVID-19 cases. Data from the Johns Hopkins Hospital System (JHHS) showed that enterovirus/rhinovirus had also been circulating at high rates. Analyzing clinical outcomes of the most prevalent respiratory viruses is crucial for understanding the role of circulating viral genotypes. A retrospective cohort of patients who tested positive for SARS-CoV-2, influenza, RSV, or enterovirus/rhinovirus between 1 June and 31 December 2023 was included in the study. Remnant clinical samples were utilized for targeted viral whole-genome sequencing and genotyping. Patients’ metadata and outcomes following infection were studied, stratified by viral variants and genotypes. The increase of SARS-CoV-2 positivity in December was associated with the predominance of JN.1. Admissions for patients under 18 years old were primarily associated with enterovirus/rhinovirus and RSV, while older age groups were mainly linked to SARS-CoV-2 and influenza infections. SARS-CoV-2-related admissions increased with the predominance of the JN.1 variant in December. No significant difference in admissions for influenza subtypes, rhinovirus species, or SARS-CoV-2 variants was observed. RSV A was associated with slightly higher odds of admission compared with RSV B. Our data highlight the importance of systematically analyzing respiratory viral infections to inform public health strategies and clinical management, especially as SARS-CoV-2 becomes endemic. The findings highlight the value of expanded genomic surveillance in elucidating the clinical significance of viral evolution.

IMPORTANCE

The analysis of the epidemiology and clinical outcomes of multiple co-circulating respiratory viruses in the early 2023/2024 respiratory virus season highlights the emergence of the SARS-CoV-2 JN.1 variant as well as underscores the importance of enterovirus/rhinovirus in respiratory infections. Understanding these dynamics is essential for refining public health strategies and clinical management, especially as SARS-CoV-2 transitions to an endemic status. This work emphasizes the need for ongoing surveillance, robust diagnostic algorithms, and detailed genomic analyses to anticipate and mitigate the burden of respiratory viral infections, ultimately contributing to more informed decision-making in healthcare settings and better patient outcomes.
The mitochondrial protein Bcs1A regulates antifungal drug tolerance by affecting efflux pump expression in the filamentous pathogenic fungus
Aspergillus fumigatus
Authors: Yang Guorong , Shi Weiwei , He Wenlin , Wu Jing , Huang Sutao , Mo Li , Zhang Junjie , Wang Huaxue , Zhou Xiaogang
Published: August 2024

Aspergillus fumigatus
is the predominant pathogen responsible for aspergillosis infections, with emerging drug-resistant strains complicating treatment strategies. The role of mitochondrial functionality in fungal resistance to antifungal agents is well-documented yet not fully understood. In this study, the mitochondrial protein Bcs1A, a homolog of yeast Bcs1, was found to regulate colony growth, ion homeostasis, and the response to antifungal drugs in
A. fumigatus
. Microscopic observations revealed substantial colocalization of Bcs1A-GFP fusion protein fluorescence with mitochondria. Bcs1A deletion compromised colony growth and the utilization of non-fermentable carbon sources, alongside causing abnormal mitochondrial membrane potential and reduced reactive oxygen species production. These findings underscore Bcs1A’s vital role in maintaining mitochondrial integrity. Phenotypic analysis and determinations of minimum inhibitory concentrations indicated that the Δ
bcs1A
mutant was more resistant to various antifungal agents, such as azoles, terbinafine, and simvastatin, compared to wild-type strain. RNA sequencing and RT-qPCR analysis highlighted an upregulation of multiple efflux pumps in the Δ
bcs1A
mutant. Furthermore, loss of the principal drug efflux pump, mdr1, decreased azole tolerance in the Δbcs1A mutant, suggesting that Bcs1A’s modulated of azoles response via efflux pump expression. Collectively, these results establish Bcs1A as essential for growth and antifungal drug responsiveness in
A. fumigatus
mediated through mitochondrial regulation.

IMPORTANCE

Drug resistance presents a formidable obstacle in the clinical management of aspergillosis. Mitochondria are integral to various biochemical pathways, including those involved in fungi drug response, making mitochondrial proteins promising therapeutic targets for drug therapy. This study confirms that Bcs1A, a mitochondrial respiratory chain protein, is indispensable for mitochondrial functionality and multidrug tolerance in
Aspergillus fumigatus
. Mutation of Bcs1A not only leads to a series of drug efflux pumps upregulated but also shows that loss of the primary efflux pump,
mdr1
, partial reduction in drug tolerance in the Bcs1A mutant, highlighting that Bcs1A’s significant influence on mitochondria-mediated drug resistance.
Rapid differentiation of
Staphylococcus aureus
in blood cultures using the STAPH score: a prospective observational study
Authors: Hayashi Toshimasa , Yoshida Masakazu
Published: August 2024

Rapid and accurate identification of
Staphylococcus aureus
(SA) in blood culture specimens is crucial for timely clinical intervention. Traditional Gram staining methods, although widely accessible and cost-effective, exhibit variable sensitivities and specificities in the BACTEC system. We aimed to develop and validate the “STAPH score,” a novel semi-quantitative scoring system that integrates Gram stain morphology and time to positivity to differentiate SA from coagulase-negative staphylococci (CoNS) in blood cultures. We analyzed 148 blood culture specimens from septic patients. Each specimen was assessed independently by two examiners using Gram staining and the STAPH score, which assigns points based on five parameters: cluster size, time to positivity, aerobic enlargement, pint (three-dimensional appearance), and the presence of hemorrhage. Sensitivity and specificity were calculated for various cutoff points. Cohen’s kappa coefficient was used to assess inter-examiner agreement. Of the 148 specimens, 49 (33.1%) were identified as SA and 99 (66.9%) as CoNS. At a STAPH score cutoff of 3 points, the sensitivity was 93.9% (95% confidence interval [CI], 83.1%–98.7%) and specificity was 91.9% (95% CI, 84.7%–96.4%). The kappa coefficient at this cutoff was 0.67 (95% CI, 0.55–0.79). A STAPH score <3 effectively ruled out SA with 100% sensitivity, whereas a score of 5 confirmed SA with 100% specificity. The STAPH score is a reliable and efficient tool for the rapid identification of SA in blood cultures within the BACTEC system. By combining Gram staining observations with time to positivity, this method enhances diagnostic accuracy, reduces subjectivity, and supports timely clinical decision-making.

IMPORTANCE

The rapid and accurate identification of
Staphylococcus aureus
(SA) in blood cultures is vital for timely and appropriate clinical intervention. This study introduces the “STAPH score,” a novel semi-quantitative scoring system that combines Gram stain morphology and time to positivity. By providing a reliable and efficient method to differentiate SA from coagulase-negative staphylococci, the STAPH score enhances diagnostic accuracy and reduces subjectivity in microscopic examinations. This score, applicable within the BACTEC system, addresses the limitations of traditional Gram staining methods and expensive molecular techniques. The implementation of the STAPH score in clinical practice can lead to faster diagnosis, improved patient outcomes, and optimized antimicrobial therapy. This method is particularly valuable in resource-limited settings where advanced diagnostic tools may not be available.
Evaluation of nikkomycin Z with frequent oral administration in an experimental model of central nervous system coccidioidomycosis
Authors: Wiederhold Nathan P. , Najvar Laura K. , Jaramillo Rosie , Olivo Marcos , Larwood David J. , Patterson Thomas F.
Published: August 2024

We evaluated the
in vivo
activity of nikkomycin Z against central nervous system coccidioidomycosis. Mice were inoculated intracranially with arthroconidia of
Coccidoides immitis
, and treatment with nikkomycin Z (50, 100, or 300 mg/kg orally TID) or fluconazole (25 mg/kg orally BID) began 2 days later. Each dose of nikkomycin Z and fluconazole significantly improved survival and reduced brain fungal burden compared with vehicle control. Further studies of nikkomycin Z against coccidioidomycosis are warranted.

IMPORTANCE

Coccidioides
species are endemic fungi that are capable of causing disease in patients with various comorbidities, as well as in otherwise healthy individuals. Treatment options for coccidioidomycosis are suboptimal, as azole antifungals may be limited by drug interactions and adverse effects due to interactions with enzymes found in humans and other mammals. Nikkomycin Z is an investigational agent that works against a target specific to the fungal cell wall (chitin), which is not present in the cells of humans or other mammals. In this study, we show that frequent oral administration of nikkomycin Z is effective in an experimental model of central nervous system coccidioidomycosis. Further studies of nikkomycin Z against coccidioidomycosis may be warranted.
Classification of
Latilactobacillus sakei
subspecies based on MALDI-TOF MS protein profiles using machine learning models
Authors: Kim Eiseul , Yang Seung-Min , Lee So-Yun , Jung Dae-Hyun , Kim Hae-Yeong
Published: August 2024

Latilactobacillus sakei
is an important bacterial species used as a starter culture for fermented foods; however, two subspecies within this species exhibit different properties in the foods. Matrix-assisted laser desorption/ionization-time of flight mass spectrometer (MALDI-TOF MS) is the gold standard for microbial fingerprinting. However, the resolution power is down to the species level. This study was to combine MALDI-TOF mass spectra and machine learning to develop a new method to identify two
L. sakei
subspecies (
L. sakei
subsp.
sakei
and
L. sakei
subsp.
carnosus
) and non-
L
.
sakei
species. Totally, 227 strains were collected, with 908 spectra obtained via on- and off-plate protein extraction. Only 68.7% of strains were correctly identified at the subspecies level in the Biotyper database; however, a high level of performance was observed from the machine learning models. Partial least squares-discriminant analysis (PLS-DA), principal component analysis-K-nearest neighbor (PCA-KNN), and support vector machine (SVM) demonstrated 0.823, 0.914, and 0.903 accuracies, respectively, whereas the random forest (RF) achieved an accuracy of 0.954, with an area under the receiver operating characteristic (AUROC) curve of 0.99, outperforming the other algorithms in distinguishing the subspecies. The machine learning proved to be a promising technique for the rapid and high-resolution classification of
L. sakei
subspecies using MALDI-TOF MS.

IMPORTANCE

Latilactobacillus sakei
plays a significant role in the realm of food bacteria. One particular subspecies of
L. sakei
is employed as a protective agent during food fermentation, whereas another strain is responsible for food spoilage. Hence, it is crucial to precisely differentiate between the two subspecies of
L. sakei
. In this study, machine learning models based on protein mass peaks were developed for the first time to distinguish
L. sakei
subspecies. Furthermore, the efficacy of three commonly used machine learning algorithms for microbial classification was evaluated. Our results provide the foundation for future research on developing machine learning models for the classification of microbial species or subspecies. In addition, the developed model can be used in the food industry to monitor
L. sakei
subspecies in fermented foods in a time- and cost-effective method for food quality and safety.
Coexistence of plasmid-mediated
tmexCD2-toprJ2
,
bla
IMP-4
, and
bla
NDM-1
in
Klebsiella quasipneumoniae
Authors: Ma Zhexiao , Qian Changrui , Yao Zhuocheng , Tang Miran , Chen Kaixin , Zhao Deyi , Hu Panjie , Zhou Tieli , Cao Jianming
Published: August 2024

Klebsiella quasipneumoniae
is a potential pathogen that has not been studied comprehensively. The emergence of multidrug-resistant (MDR)
K. quasipneumoniae
, specifically strains resistant to tigecycline and carbapenem, presents a significant challenge to clinical treatment. This investigation aimed to characterize MDR
K. quasipneumoniae
strain FK8966, co-carrying
tmexCD2-toprJ2
,
bla
IMP-4
, and
bla
NDM-1
by plasmids. It was observed that FK8966’s MDR was primarily because of the IncHI1B-like plasmid co-carrying
tmexCD2-toprJ2
and
bla
IMP-4
, and an IncFIB(K)/IncFII(K) plasmid harboring
bla
NDM-1
. Furthermore, the phylogenetic analysis revealed that IncHI1B-like plasmids carrying
tmexCD2-toprJ2
were disseminated among different bacteria, specifically in China. Additionally, according to the comparative genomic analysis, the MDR regions indicated that the
tmexCD2-toprJ2
gene cluster was inserted into the
umuC
gene, while
bla
IMP-4
was present in transposon Tn
As3
linked to the class 1 integron (
IntI1
). It was also observed that an ΔTn
3000
insertion with
bla
NDM-1
made a novel
bla
NDM-1
harboring IncFIB(K)/IncFII(K) plasmid. The antimicrobial resistance prevalence and phylogenetic analyses of
K. quasipneumoniae
strains indicated that FK8966 is a distinct MDR branch of
K. quasipneumoniae
. Furthermore, CRISPR-Cas system analysis showed that many
K. quasipneumoniae
CRISPR-Cas systems lacked spacers matching the two aforementioned novel resistance plasmids, suggesting that these resistance plasmids have the potential to disseminate within
K. quasipneumoniae
. Therefore, the spread of MDR
K. quasipneumoniae
and plasmids warrants further attention.

IMPORTANCE

The emergence of multidrug-resistant
K. quasipneumoniae
poses a great threat to clinical care, and the situation is exacerbated by the dissemination of tigecycline- and carbapenem-resistant genes. Therefore, monitoring these pathogens and their resistance plasmids is urgent and crucial. This study identified tigecycline- and carbapenem-resistant
K. quasipneumoniae
strain, FK8966. Furthermore, it is the first study to report the coexistence of
tmexCD2-toprJ2
,
bla
IMP-4
, and
bla
NDM-1
in
K. quasipneumoniae
. Moreover, the CRISPR-Cas system of many
K. quasipneumoniae
lacks spacers that match the plasmids carried by FK8966, which are crucial for mediating resistance against tigecycline and carbapenems, indicating their potential to disseminate within
K. quasipneumoniae
.
Staphylococcal
sRNA IsrR downregulates methylthiotransferase MiaB under iron-deficient conditions
Authors: Barrault Maxime , Leclair Elise , Kumeko Etornam Kofi , Jacquet Eric , Bouloc Philippe
Published: August 2024

Staphylococcus aureus
is a major contributor to bacterial-associated mortality, owing to its exceptional adaptability across diverse environments. Iron is vital to most organisms but can be toxic in excess. To manage its intracellular iron,
S. aureus
, like many pathogens, employs intricate systems. We have recently identified IsrR as a key regulatory RNA induced during iron starvation. Its role is to reduce the synthesis of non-essential iron-containing proteins under iron-depleted conditions. In this study, we unveil IsrR’s regulatory action on MiaB, an enzyme responsible for methylthio group addition to specific sites on transfer RNAs (tRNAs). We use predictive tools and reporter fusion assays to demonstrate IsrR’s binding to the Shine-Dalgarno sequence of
miaB
RNA, thereby impeding its translation. The effectiveness of IsrR hinges on the integrity of a specific C-rich region. As MiaB is non-essential and has iron-sulfur clusters, IsrR induction spares iron by downregulating
miaB
. This may improve
S. aureus
fitness and aid in navigating the host’s nutritional immune defenses.

IMPORTANCE

In many biotopes, including those found within an infected host, bacteria confront the challenge of iron deficiency. They employ various strategies to adapt to this scarcity of nutrients, one of which involves regulating iron-containing proteins through the action of small regulatory RNAs. Our study shows how IsrR, a small RNA from
S. aureus
, prevents the production of MiaB, a tRNA-modifying enzyme containing iron-sulfur clusters. With this illustration, we propose a new substrate for an iron-sparing small RNA, which, when downregulated, should reduce the need for iron and save it to essential functions.
An interlaboratory proficiency test using metagenomic sequencing as a diagnostic tool for the detection of RNA viruses in swine fecal material
Authors: Liu Lihong , Hakhverdyan Mikhayil , Wallgren Per , Vanneste Kevin , Fu Qiang , Lucas Pierrick , Blanchard Yannick , de Graaf Miranda , Oude Munnink Bas B. , van Boheemen Sander , Bossers Alex , Hulst Marcel , Van Borm Steven
Published: August 2024

Metagenomic shotgun sequencing (mNGS) can serve as a generic molecular diagnostic tool. An mNGS proficiency test (PT) was performed in six European veterinary and public health laboratories to detect porcine astroviruses in fecal material and the extracted RNA. While different mNGS workflows for the generation of mNGS data were used in the different laboratories, the bioinformatic analysis was standardized using a metagenomic read classifier as well as read mapping to selected astroviral reference genomes to assess the semiquantitative representation of astrovirus species mixtures. All participants successfully identified and classified most of the viral reads to the two dominant species. The normalized read counts obtained by aligning reads to astrovirus reference genomes by Bowtie2 were in line with Kraken read classification counts. Moreover, participants performed well in terms of repeatability when the fecal sample was tested in duplicate. However, the normalized read counts per detected astrovirus species differed substantially between participants, which was related to the different laboratory methods used for data generation. Further modeling of the mNGS data indicated the importance of selecting appropriate reference data for mNGS read classification. As virus- or sample-specific biases may apply, caution is needed when extrapolating this swine feces-based PT for the detection of other RNA viruses or using different sample types. The suitability of experimental design to a given pathogen/sample matrix combination, quality assurance, interpretation, and follow-up investigation remain critical factors for the diagnostic interpretation of mNGS results.

IMPORTANCE

Metagenomic shotgun sequencing (mNGS) is a generic molecular diagnostic method, involving laboratory preparation of samples, sequencing, bioinformatic analysis of millions of short sequences, and interpretation of the results. In this paper, we investigated the performance of mNGS on the detection of porcine astroviruses, a model for RNA viruses in a pig fecal material, among six European veterinary and public health laboratories. We showed that different methods for data generation affect mNGS performance among participants and that the selection of reference genomes is crucial for read classification. Follow-up investigation remains a critical factor for the diagnostic interpretation of mNGS results. The paper contributes to potential improvements of mNGS as a diagnostic tool in clinical settings.
Application of the IOC Relative Energy Deficiency in Sport (REDs) Clinical Assessment Tool version 2 (CAT2) across 200+ elite athletes
Authors: Heikura Ida A , McCluskey Walter T P , Tsai Ming-Chang , Johnson Liz , Murray Holly , Mountjoy Margo , Ackerman Kathryn E , Fliss Matthew , Stellingwerff Trent
Published: August 2024

Objective

This cross-sectional retrospective and prospective study implemented the 2023 International Olympic Committee Relative Energy Deficiency in Sport (REDs) Clinical Assessment Tool version 2 (CAT2) to determine the current severity of REDs (primary outcome) and future risk of bone stress injuries (BSI, exploratory outcome) in elite athletes.

Methods

Female (n=143; 23.3±4.3 years) and male (n=70; 23.1±3.7 years) athletes (performance tier 3 (52%), tier 4 (36%), tier 5 (12%)) participated in a baseline CAT2 (with minor modifications) assessment, including a self-report questionnaire (menstrual function (females), BSI, Eating Disorder Examination Questionnaire (EDE-Q)), bone mineral density (BMD via DXA) and fasted blood analysis (triiodothyronine (T3), testosterone, cholesterol). Athletes were assigned a green, yellow, orange or red light via CAT2. The prospective risk of new self-report of physician-diagnosed BSI was assessed over a subsequent 6–24 months.

Results

REDs prevalence was 55% green, 36% yellow, 5% orange and 4% red light. The CAT2 identified a greater prevalence of amenorrhoea and BSI and lower T3, testosterone and BMD (p<0.01) in red, orange and yellow (those with REDs) versus green light. ORs for a prospective self-reported BSI (majority physician diagnosed) were greater in orange vs green (OR 7.71, 95% CI (1.26 to 39.83)), in females with severe amenorrhoea (OR 4.6 (95% CI 0.98 to 17.85)), in males with low sex drive (OR 16.0 (95% CI 4.79 to 1038.87)), and athletes with elevated EDE-Q global scores (OR 1.45 (95% CI 0.97 to 1.97)).

Conclusion

The CAT2 has high validity in demonstrating current severity of REDs, with increased future risk of self-reported BSI in athletes with a more severe REDs traffic light category.
Next-generation rheumatoid factor assay provides improved predictive power for the development of arthritis in patients at risk
Authors: Oskam Nienke , Ooijevaar-de Heer Pleuni , Kos Dorien , van Boheemen Laurette , van Schaardenburg Dirkjan , Wolbink Gertjan , Rispens Theo
Published: August 2024

Objective

Rheumatoid arthritis (RA) is characterised by the presence of autoantibodies, among which those targeting the constant region of immunoglobulin G (IgG), called rheumatoid factors (RF). Despite this link, RFs can also be found in other disorders and the healthy population, which hampers its use as a diagnostic tool. We recently showed that a subset of RA-derived RFs target a distinct epitope on the IgG-Fc, a feature that is currently not used in the clinic.

Methods

We determined immunoglobulin M (IgM)-RF levels specific against an RA-associated epitope (using our engineered next-generation RF antigen ‘T3-17’) in a prospective cohort of 475 patients with seropositive (for IgM-RF or aCCP) arthralgia that were followed for 5 years or until the development of arthritis.

Results

The presence of RFs targeting T3-17 was more strongly associated with progression to arthritis in comparison to traditional RF measurements. Within the group of patients positive for T3-17 RF the risk of arthritis development was increased as compared with wild-type RF, HR=3.2 (95% CI 2.4 to 4.3) vs HR=2.2 (95% CI 1.7 to 3.0). Predictive power of T3-17 RF was improved in combination with aCCP titres, HR=6.4 (4.7–8.7) vs HR=5.1 (3.9–6.8). This combination performed better than aCCP detection on its own.

Conclusion

The detection of disease-specific RF is feasible and seems to improve the diagnostic power of RF and should be considered to be implemented in the clinic.
Significant decrease of osteoporosis and osteoporotic fractures in rheumatoid arthritis within a period of 24 years: experiences of a single centre
Authors: Oelzner Peter , Mueller Paul-Heinrich , Hoffmann Tobias , Schwabe Antje , Lehmann Gabriele , Eidner Thorsten , Wolf Gunter , Pfeil Alexander
Published: August 2024

Objectives

Rheumatoid arthritis (RA) is associated with an increased risk for osteoporosis and osteoporotic fractures. Since the treatment of RA has improved significantly in recent years, we can expect RA-associated osteoporosis to decrease with good disease control. Therefore, we conducted a retrospective study to investigate whether the frequency of osteoporosis and osteoporotic fractures has changed during 24 years in RA.

Methods

We analysed the data of 1.086 RA patients from the time of the first osteological assessment with bone mineral density (BMD) measurement and collection of osteologically important data during the years 1996 and 2019 at our clinic. According to the treatment period, the patients were divided into cohort 1 (investigation between 1996 and 2004; n=539) and cohort 2 (investigation between 2005 and 2019; n=547). The data of the two cohorts were compared, and predictors of BMD were analysed by linear regression analysis.

Results

Prevalence of osteoporosis (28.3% vs 48.4%; p<0.001) as well as osteoporotic peripheral fractures (11.5% vs 21%; p<0.001) and vertebral fractures (6.6% vs 10.9%; p=0.011) were significantly lower and treatment with biologicals (19.7% vs 5.0%; p<0.001) significantly more common and glucocorticoid use was significantly less common (p=0.005) in cohort 2. In RA patients with a disease duration of more than 2 years, BMD was significantly higher under treatment with biologicals (p<0.001) despite increased cumulative glucocorticoid dosages (p<0.001).

Conclusion

Our study showed a significant decline in osteoporosis and osteoporotic fractures in RA for 24 years. This positive effect is associated with the more frequent use of biologicals in the years between 2005 and 2019.
Bifurcation analysis of a diffusive radio-dependent model with spatial memory
Authors: An Qi , Gu Xingyu , Zhang Xuebing
Published: August 2024

The cognitive abilities of animals, such as memory, have a significant impact on their movement in space. In this paper, we consider a radio-dependent model with memory-based diffusion under the conditions of Neumann boundary. The stability of a positive equilibrium and the existence of the Turing–Hopf bifurcation induced by memory diffusion and memory delay are carried out in details. Notably, our findings indicate that with a relatively short average memory period, the large memory diffusion can stabilize an otherwise unstable equilibrium. In addition, the third-order truncated normal form for the Turing–Hopf bifurcation restricted to the central manifold is derived, which can reveal the generation of some steady-state and time-periodic solutions with spatial heterogeneity. The coefficients within the normal form are systematically determined through matrix operations, and these results can also be applied to other models with memory diffusion. Ultimately, leveraging the theoretical findings, we elucidated the intricate spatial-temporal dynamics and their associated parameter scopes caused by Turing–Hopf bifurcation through numerical simulations.
Early Neoproterozoic (Tonian) subduction-related magmatism and tectonothermal activity in Shetland and northern mainland Scotland: implications for the tectonic evolution of NE Laurentia and Rodinia reconstructions
Authors: Kinny P. D. , Strachan R. A. , Fowler M. B. , Bruand E. , Millar I. L. , Hand M. , Clark C. , Cutts K. A.
Published: August 2024

The tectonic setting of Tonian orogenic events recorded in the present-day circum-North Atlantic region is uncertain. U–Pb zircon geochronology shows that the Yell Sound and Westings groups (Shetland) and metasedimentary rocks of the Naver Nappe (northern mainland Scotland) were deposited between
c.
1050 and 960 Ma and intruded by mafic, intermediate and felsic igneous rocks at
c.
965–950 Ma. Chemical discrimination diagrams and Hf and Nd isotope data together suggest that the protoliths of the mafic meta-igneous rocks were emplaced as relatively juvenile crustal contributions in an active plate margin. Zircon growth at
c.
920 Ma within the Yell Sound Group correlates with high-grade metamorphism documented previously in Shetland. Further zircon growth and Pb loss at
c.
470–460 Ma indicates overprinting during the Ordovician Grampian orogenic event. Similar age successions of Ellesmere Island, Svalbard and East Greenland also contain evidence for Tonian magmatism (some calc-alkaline), deformation and metamorphism. The new data favour Rodinia reconstructions that incorporate subduction-related magmatism and associated tectonism along the margin of NE Laurentia during the Tonian. The Yell Sound Group and correlative peri-Laurentian successions were intruded by subduction-related magmas and deformed and metamorphosed during development of the Valhalla exterior accretionary orogen, part of a more extensive peri-Rodinian subduction system.
Gradient-Based Adversarial Training on Transformer Networks for Detecting Check-Worthy Factual Claims
Authors: Meng Kevin , Jimenez Damian , Devasier Jacob Daniel , Naraparaju Sai Sandeep , Arslan Fatma , Obembe Daniel , Li Chengkai
Published: August 2024

This article presents the latest developments to ClaimBuster’s claim-spotting model, which tackles the critical task of identifying check-worthy claims from large streams of information. We introduce the first adversarially regularized, transformer-based claim-spotting model, which achieves state-of-the-art results on several benchmark datasets. In addition to analyzing model performance metrics, we also quantitatively and qualitatively analyze the impact of ClaimBuster’s real-world deployment. Moreover, to help facilitate reproducibility and community engagement, we publicly release our codebase, dataset, data curation platform, API, Google Colab notebooks, and various ClaimBuster-based demo systems, at
claimbuster.org
.
Intraduodenal fecal microbiota transplantation ameliorates gut atrophy and cholestasis in a novel parenteral nutrition piglet model
Authors: Manithody Chandrashekhara , Denton Christine , Mehta Shaurya , Carter Jasmine , Kurashima Kento , Bagwe Ashlesha , Swiderska-Syn Marzena , Guzman Miguel , Besmer Sherri , Jain Sonali , McHale Matthew , Qureshi Kamran , Nazzal Mustafa , Caliskan Yasar , Long John , Lin Chien-Jung , Hutchinson Chelsea , Ericsson Aaron C. , Jain Ajay Kumar
Published: August 2024

Intraduodenal fecal microbiota transplantation presents a novel strategy to mitigate complications associated with total parenteral nutrition (TPN), highlighting gut microbiota as a prime target for therapeutic and diagnostic approaches. These results from a highly translatable model provide hope for TPN side effect mitigation for thousands of chronically TPN-dependent patients.
Durability of motor learning by observing
Authors: Mangos Natalia , Forgaard Christopher J. , Gribble Paul L.
Published: August 2024

We used force channel probes in an upper limb force-field reaching task in humans to compare the durability of learning-related changes that occurred through visual observation to those after physical movement practice. Visually acquired representations of movement dynamics continued to influence behavior for at least 1 h after observation. Our findings point to a 1-h window during which visual observation of another person could play a role in motor learning.
Effect of Different Surfactants and Nanoparticles on Pore‐Scale Oil Recovery Process Using Heterogeneous Micromodel
Authors: Liu Yafei , Liu Zhike , Wang Yibo , Hu Zhangpeng , Zhu Zhehan , Jie Yenan , Zhang Yanjun
Published: August 2024

The application of surface‐active agents during oil recovery process is ubiquitous. It is essential to achieve a satisfying oil recovery rate with low dosage of surface‐active substances in an environment‐friendly manner. Despite the wide application of surface‐active agents, the impact of individual and the combination of surface‐active agents on the microscale multiphase flow and interfacial phenomenon have not been systematically investigated. In this work, idealized pore‐throat network micromodels were employed as the surrogate of the porous media to study the influence of surface‐active agents on the oil recovery involving nonionic, anionic, zwitterionic surfactants, and nanoparticles. Oil recovery efficiency and residual oil characteristic in different permeable regions were quantitatively analyzed. Anionic surfactants resulted in the highest oil recovery of 79% and were selected to formulate composite agents. The combination of anionic and zwitterionic surfactants resulted in better overall oil recovery which was up to 84%, yet complicated interfacial phenomenon was observed. To comprehend the complex interactions between crude oil and assorted surface‐active agents, the impact of interfacial tension, wettability, and emulsification on oil‐brine flow behaviors and final oil recovery was discussed providing an insight on the efficient and cost‐effective application of surface‐active agents on enhancing oil recovery.
Numerical Study of the Boundary Layer Separation of a Low‐Pressure Turbine Cascade at Different Incidence Angles
Authors: Bao Tianwei , He Zhengyang , Du Jiale , Wang Chengyan , Fang Le , Chen Song
Published: August 2024

Modern low‐pressure turbine (LPT) pursues high blade loading to improve its efficiency while the possibility of boundary layer separation on the blades is still a challenging problem. The incidence angle is one of the main factors affecting the flow separation and laminar‐turbulent transition, which is of key importance for the design of LPT. In this work, based on the initial simulation results obtained using the Reynolds‐averaged Navier–Stokes (RANS) method, the flow past a single LPT cascade at three representative incident angles (i = −10°, 0°, +10°) is investigated using large‐eddy simulation (LES) method with approximately 26 million structured grids. The simulations are carried out with Open Source Field Operation and Manipulation (OpenFOAM) for an off‐design low Reynolds number condition Re = 40,000 and Ma = 0.5. The time‐averaged aerodynamic performances and three‐dimensional instantaneous flow characteristics of the LPT cascade are discussed in detail, and the results show that the blade loading and the transverse pressure gradient (TPG) from the pressure side to the suction side of leading edge (LE) increase with increasing incidence angle. At the incidence angle of +10°, the LPT cascade undergoes separation and reattachment from the LE to around 20% Cax on the suction surface, which weakens the separation phenomenon at the rear half of the suction surface and the total pressure loss downstream of the trailing edge (TE). It is worth noting that the RANS method underpredicts the blade boundary layer separation region compared with LES under these extreme conditions. These results may offer off‐design condition data for the future improvement of RANS models or experimental studies.
Supplementary Figure S8 from Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma
Authors: Johanns Tanner M. , Garfinkle Elizabeth A.R. , Miller Katherine E. , Livingstone Alexandra J. , Roberts Kaleigh F. , Rao Venkata Lakshmi P. , Dowling Joshua L. , Chicoine Michael R. , Dacey Ralph G. , Zipfel Gregory J. , Kim Albert H. , Mardis Elaine R. , Dunn Gavin P.
Published: August 2024

CDR3beta sequences ranked by ratio