bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid differentiation of
Staphylococcus aureus
in blood cultures using the STAPH score: a prospective observational study
Authors: Hayashi Toshimasa , Yoshida Masakazu 
Published: August 2024

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ObjectiveThis 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.MethodsFemale (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.ResultsREDs 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)).ConclusionThe 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

ObjectiveRheumatoid 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.MethodsWe 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.ResultsThe 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.ConclusionThe 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

ObjectivesRheumatoid 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.MethodsWe 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.ResultsPrevalence 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).ConclusionOur 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.
Trametinib Potentiates Anti-PD-1 Efficacy in Tumors Established from Chemotherapy-Primed Pancreatic Cancer Cells
Authors: Pham Thao D. , Metropulos Anastasia E. , Mubin Nida , Becker Jeffrey H. , Shah Dhavan , Spaulding Christina , Shields Mario A. , Bentrem David J. , Munshi Hidayatullah G. 
Published: August 2024

Abstract
Despite advances in immune checkpoint inhibitors, chemotherapy remains the standard therapy for patients with pancreatic ductal adenocarcinoma (PDAC). As the combinations of chemotherapy, including the FOLFIRINOX [5-fluorouracil, F; irinotecan, I; and oxaliplatin, O (FIO)] regimen, and immune checkpoint inhibitors have failed to demonstrate clinical benefit in patients with metastatic PDAC tumors, there is increasing interest in identifying therapeutic approaches to potentiate ICI efficacy in patients with PDAC. In this study, we report that neoadjuvant FOLFIRINOX-treated human PDAC tumors exhibit increased MEK/ERK activation. We also show elevated MEK/ERK signaling in ex vivo PDAC slice cultures and cell lines treated with a combination of FIO. In addition, we find that the KPC-FIO cells, established from repeated treatment of mouse PDAC cell lines with six to eight cycles of FIO, display enhanced ERK phosphorylation and demonstrate increased sensitivity to MEK inhibition in vitro and in vivo. Significantly, the KPC-FIO cells develop tumors with a proinflammatory immune profile similar to human PDAC tumors after neoadjuvant FOLFIRINOX treatment. Furthermore, we found that the MEK inhibitor trametinib enables additional infiltration of highly functional CD8+ T cells into the KPC-FIO tumors and potentiates the efficacy of anti-PD-1 antibody in syngeneic mouse models. Our findings provide a rationale for combining trametinib and anti-PD-1 antibodies in patients with PDAC after neoadjuvant or short-term FOLFIRINOX treatment to achieve effective antitumor responses.