bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mouse and human immune responses share neutralization epitopes of HAstV-VA1
Authors: Ramírez-Bello Inci , López Tomás , Espinosa Rafaela , Ghosh Anisa , Green Kassidy , Riaño-Umbarila Lidia , Gaspar-Castillo Carlos , Aguilera-Flores Catalina , Alpuche-Aranda Celia M. , López Susana , DuBois Rebecca M. , Arias Carlos F. 
Published: June 2024

ABSTRACT

Astroviruses are highly divergent and infect a wide variety of animal hosts. In 2009, a genetically divergent human astrovirus (HAstV) strain VA1 was first identified in an outbreak of acute gastroenteritis. This strain has also been associated with fatal central nervous system disease. In this work, we report the isolation of three high-affinity neutralizing monoclonal antibodies (Nt-MAbs) targeting the capsid spike domain of HAstV-VA1. These antibodies (7C8, 2A2, 3D8) were used to select individual HAstV-VA1 mutants resistant to their neutralizing activity and a HAstV-VA1 triple mutant that escapes neutralization from all three Nt-MAbs. Sequencing of the virus genome capsid region revealed escape mutations that map to the surface of the capsid spike domain, define three potentially independent neutralization epitopes, and help delineate four antigenic sites in human astroviruses. Notably, two of the escape mutations were found to be present in the spike sequence of the HAstV-VA1-PS strain isolated from an immunodeficient patient with encephalitis, suggesting that those mutations arose as a result of the immune pressure generated by the patient’s immunotherapy. In agreement with this observation, human serum samples exhibiting strong neutralization activity against wild-type HAstV-VA1 had a 2.6-fold reduction in neutralization titer when evaluated against the triple-escape HAstV-VA1 mutant, suggesting that both mouse and human antibody responses target shared neutralization epitopes. The isolated Nt-MAbs reported in this work will help to characterize the functional domains of the virus during cell entry and have the potential for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1.

IMPORTANCE
Human astroviruses (HAstVs) have been historically associated with acute gastroenteritis. However, the genetically divergent HAstV-VA1 strain has been associated with central nervous system disease. In this work high-affinity neutralizing monoclonal antibodies directed to HAstV-VA1 were isolated and characterized. The proposed binding sites for these antibodies and for neutralizing antibodies against classical HAstVs suggest that there are at least four neutralization sites on the capsid spike of astroviruses. Our data show that natural infection with human astrovirus VA1 elicits a robust humoral immune response that targets the same antigenic sites recognized by the mouse monoclonal antibodies and strongly suggests the emergence of a variant HAstV-VA1 virus in an immunodeficient patient with prolonged astrovirus infection. The isolated Nt-MAb reported in this work will help to define the functional sites of the virus involved in cell entry and hold promise for developing a specific antibody therapy for the neurological disease associated with HAstV-VA1.
Define SNP thresholds for delineation of tuberculosis transmissions using whole-genome sequencing
Authors: Xiao Yu-Xin , Chan Tai-Hua , Liu Kuang-Hung , Jou Ruwen 
Published: June 2024

ABSTRACT

For facilitating tuberculosis (TB) control, we used a whole-genome sequencing (WGS)-based approach to delineate transmission networks in a country with an intermediate burden of TB. A cluster was defined as
Mycobacterium tuberculosis
isolates with identical genotypes, and an outbreak was defined as clustered cases with epidemiological links (epi-links). To refine a cluster predefined using space oligonucleotide typing and mycobacterial interspersed repetitive unit variable tandem repeat typing, we analyzed one pansusceptible TB (C1) and three multidrug-resistant (MDR)-TB (C2-C4) clusters from different scenarios. Pansusceptible TB cluster (C1) consisting of 28 cases had ≤5 single nucleotide polymorphisms (SNPs) difference between their isolates. C1 was a definite outbreak, with cases attending the same junior high school in 2012. Three MDR-TB clusters (C2-C4) with distinct genotypes were identified, each consisting of 12–22 cases. Some of the cases had either ≤5 or ≤15 SNPs difference with clear or probable epi-links. Of note, even though WGS could effectively assist TB contact tracing, we still observed missing epi-links in some cases within the same cluster. Our results showed that thresholds of ≤5 and ≤15 SNPs difference between isolates were used to categorize definite and probable TB transmission, respectively. Furthermore, a higher SNP threshold might be required to define an MDR-TB outbreak. WGS still needs to be combined with classical epidemiological methods for improving outbreak investigations. Importantly, different SNP thresholds have to be applied to define outbreaks.

IMPORTANCE

TB is a chronic disease. Depending on host factors and TB burden, clusters of cases may continue to increase for several years. Conventional genotyping methods overestimate TB transmission, hampering precise detection of outbreaks and comprehensive surveillance. WGS can be used to obtain SNP information of
M. tuberculosis
to improve discriminative limitations of conventional methods and to strengthen delineation of transmission networks. It is important to define the country-specific SNP thresholds for investigation of transmission. This study demonstrated the use of thresholds of ≤5 and ≤15 SNPs difference between isolates to categorize definite and probable transmission, respectively. Different SNP thresholds should be applied while a higher cutoff was required to define an MDR-TB outbreak. The utilization of SNP thresholds proves to be crucial for guiding public health interventions, eliminating the need for unnecessary public health actions, and potentially uncovering undisclosed TB transmissions.
A
Mycobacterium ulcerans
vaccine pilot trial using an accurate low-dose challenge
Authors: Muhi Stephen , Porter Jessica L. , Stinear Timothy P. 
Published: June 2024

ABSTRACT

A
Mycobacterium ulcerans
human challenge model has the potential to fundamentally advance our understanding of early human immune responses to infection, while rapidly evaluating vaccines and other therapeutic interventions. Here, using a murine tail infection model, we tested a very well-characterized working cell bank of the proposed challenge isolate
M. ulcerans
JKD8049 in naïve and
Mycobacterium bovis
bacille Calmette–Guérin (BCG)-vaccinated BALB/c mice. All 10 naïve mice were successfully infected with 20 colony-forming units (CFU) of
M. ulcerans
[95% confidence interval (CI) 17–22 CFU] with a mean time to visible lesion of 86 days (95% CI 79–92 days). In the 10 vaccinated mice, there was a significant delay in the mean time to lesion compared to the naïve controls of 24 days (
P
= 0.0003), but all mice eventually developed ulcerative lesions. This study informs a future human infection model by demonstrating the successful application of the challenge agent in this
in vivo
model and highlights both the promise and the problems with trying to induce protective immunity against
M. ulcerans
.

IMPORTANCE

In preparation for its proposed use in a controlled human infection model (CHIM), this study reports the successful infection of BALB/c mice using a carefully characterized, low-dose inoculum of
Mycobacterium ulcerans
JKD8049 (our proposed CHIM strain). We also demonstrate that
Mycobacterium bovis
bacille Calmette–Guérin delays the onset of disease but cannot alter the course of illness once a lesion becomes apparent. We also validate the findings of previous low-dose challenges that used less accurate methods to determine the inoculum, but our presented methodology is practical, accurate, and anticipated to be reproducible.
Changing epidemiology and antimicrobial resistance of bacteria causing bacteremia in Taiwan: 2002–2020
Authors: Huang Ying-Chi , Kuo Shu-Chen , Fang Chi-Tai , Lauderdale Tsai-Ling 
Published: June 2024

ABSTRACT

Bacteremia is associated with significant morbidity and mortality. The emergence of bacteria with antimicrobial resistance (AMR) has further exacerbated the poor outcomes associated with bacteremia. The Taiwan Surveillance of Antimicrobial Resistance (TSAR) program was established in 1998 to monitor bacterial epidemiology and antimicrobial resistance trends across all patient types and age groups. Between 2002 and 2020, a total of 14,539 non-duplicate bacteremia isolates were collected biennially from 29 hospitals during the months of July–September as part of the TSAR program. The three most common bacteremia agents were
Escherichia coli
(31%),
Staphylococcus aureus
(13.6%), and
Klebsiella pneumoniae
(12.7%) overall. However, there was a steady increase in the proportions of
E. coli
and
Enterococcus faecium
isolated from bacteremia cases (both
P
< 0.001), while the proportions of
Acinetobacter
spp. decreased. Regarding antimicrobial resistance, there was a notable increase in rates of third-generation cephalosporin and fluoroquinolone non-susceptibility among
E. coli
and
K. pneumoniae
, while the rates of carbapenem non-susceptibility were elevated but remained milder in these two species, especially in
E. coli
. Of concern is the alarming increase in vancomycin resistance among
E. faecium
, rising from 10.0% in 2004 to 47.7% in 2020. In contrast, the prevalence of methicillin-resistant
S. aureus
has remained stable at 51.2% overall. In conclusion,
E. coli
, with increasing third-generation cephalosporin and fluoroquinolone resistance, is the predominant cause of bacteremia in Taiwan during the 18-year surveillance. The escalating proportion of
E. faecium
in bacteremia, coupled with a concurrent upsurge in vancomycin resistance, presents a therapeutic challenge in the recent decade.

IMPORTANCE

AMR surveillance not only enables the identification of regional variations but also supports the development of coordinated efforts to combat AMR on a global scale. The TSAR has been a biennial, government-endorsed, multicenter study focusing on pathogens isolated from inpatients and outpatients in Taiwan hospitals since 1998. Our report presents an 18-year comprehensive analysis on blood isolates in the 2002–2020 TSAR program. The study highlights an alarming increase in the proportion of
E. faecium
causing bacteremia accompanied by elevated vancomycin resistance. It is worth noting that this trend differs from the observations in the United States and China. Understanding the composition of bacteria causing bacteremia, along with their prevalence of antimicrobial resistance, holds significant importance in establishing healthcare and research priorities. Additionally, this knowledge serves as a critical factor in evaluating the effectiveness of preventive interventions.
Enrichment of Terbium(III) under synergistic effect of biosorption and biomineralization by
Bacillus
sp. DW015 and
Sporosarcina pasteurii
Authors: Bian Zijun , Dong Wei , Li Xi , Song Yuexin , Huang Huihong , Hong Kemin , Hu Kaijian 
Published: June 2024

ABSTRACT

Biosorption and biomineralization are commonly used for the immobilization of metal ions. Biosorption is commonly used as a green method to enrich rare earth ions from wastewater. However, little attention has been paid to the facilitating role of biomineralization in the enrichment of rare earth ions. In this study, a strain of
Bacillus
sp. DW015, isolated from ion adsorption type rare earth ores and a urease-producing strain
Sporosarcina pasteurii
were used to enrich rare earth elements (REEs) from an aqueous solution. The results indicate that biomineralization accelerates the enrichment of Terbium(III) compared to biosorption alone. Kinetic analysis suggests that the main mode of action of DW015 was biosorption, following pseudo-second-order kinetics (
R
2
= 0.998). The biomineralization of DW015 did not significantly contribute to the enrichment of Tb(III), whereas excessive biomineralization of
S. pasteurii
led to a decrease in the enrichment of Tb(III). A synergistic system of biosorption and biomineralization was established by combining the two bacteria, with the optimal mixed bacteria (
S. pasteurii
:DW015) ratio being 1:19. This study provides fundamental support for the synergistic effect of biosorption and biomineralization and offers a new reference for future microbial-based enrichment methods.

IMPORTANCE

A weak microbially induced calcium carbonate precipitation (MICP) promotes the enrichment of Tb(III) by bacteria, while a strong MICP leads to the release of Tb(III). However, existing explanations cannot elucidate these mechanisms. In this study, the morphology of the bioprecipitation and the degree of Tb(III) enrichment were analyzed by X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDS). The data revealed that MICP could drive stable attachment of Tb(III) onto the cell surface, forming a Tb-CaCO
3
mixed solid phase. Excessive rapid rate of calcite generation could disrupt the Tb(III) adsorption equilibrium, leading to the release of Tb(III). Therefore, in order for Tb(III) to be stably embedded in calcite, it is necessary to have a sufficient number of adsorption sites on the bacteria and to regulate the rate of MICP. This study provides theoretical support for the process design of MICP for the enrichment of rare earth ions.
Modulation of riboflavin biosynthesis and utilization in mycobacteria
Authors: Chengalroyen Melissa D. , Mehaffy Carolina , Lucas Megan , Bauer Niel , Raphela Mabule L. , Oketade Nurudeen , Warner Digby F. , Lewinsohn Deborah A. , Lewinsohn David M. , Dobos Karen M. , Mizrahi Valerie 
Published: June 2024

ABSTRACT

Riboflavin (vitamin B
2
) is the precursor of the flavin coenzymes, FAD and FMN, which play a central role in cellular redox metabolism. While humans must obtain riboflavin from dietary sources, certain microbes, including
Mycobacterium tuberculosis
(Mtb), can biosynthesize riboflavin
de novo
. Riboflavin precursors have also been implicated in the activation of mucosal-associated invariant T (MAIT) cells which recognize metabolites derived from the riboflavin biosynthesis pathway complexed to the MHC-I-like molecule, MR1. To investigate the biosynthesis and function of riboflavin and its pathway intermediates in mycobacterial metabolism and physiology, we constructed conditional knockdowns (hypomorphs) in riboflavin biosynthesis and utilization genes in
Mycobacterium smegmatis
(Msm) and Mtb by inducible CRISPR interference. Using this comprehensive panel of hypomorphs, we analyzed the impact of gene silencing on viability, on the transcription of (other) riboflavin pathway genes, on the levels of the pathway proteins, and on riboflavin itself. Our results revealed that (i) despite lacking a canonical transporter, both Msm and Mtb assimilate exogenous riboflavin when supplied at high concentration; (ii) there is functional redundancy in lumazine synthase activity in Msm; (iii) silencing of
ribA2
or
ribF
is profoundly bactericidal in Mtb; and (iv) in Msm,
ribA2
silencing results in concomitant knockdown of other pathway genes coupled with RibA2 and riboflavin depletion and is also bactericidal. In addition to their use in genetic validation of potential drug targets for tuberculosis, this collection of hypomorphs provides a useful resource for future studies investigating the role of pathway intermediates in MAIT cell recognition of mycobacteria.

IMPORTANCE

The pathway for biosynthesis and utilization of riboflavin, precursor of the essential coenzymes, FMN and FAD, is of particular interest in the flavin-rich pathogen,
Mycobacterium tuberculosis
(Mtb), for two important reasons: (i) the pathway includes potential tuberculosis (TB) drug targets and (ii) intermediates from the riboflavin biosynthesis pathway provide ligands for mucosal-associated invariant T (MAIT) cells, which have been implicated in TB pathogenesis. However, the riboflavin pathway is poorly understood in mycobacteria, which lack canonical mechanisms to transport this vitamin and to regulate flavin coenzyme homeostasis. By conditionally disrupting each step of the pathway and assessing the impact on mycobacterial viability and on the levels of the pathway proteins as well as riboflavin, our work provides genetic validation of the riboflavin pathway as a target for TB drug discovery and offers a resource for further exploring the association between riboflavin biosynthesis, MAIT cell activation, and TB infection and disease.
Clostridium sporogenes
increases fat accumulation in mice by enhancing energy absorption and adipogenesis
Authors: Du Lei , Wang Jing , Qiu Xiaoyu , Wang Qi , Peng Han , Huang Jinxiu , Yang Feiyun , Liu Zuohua , Qi Renli 
Published: June 2024

ABSTRACT

Gut bacteria belonging to the
Clostridium
family play a pivotal role in regulating host energy balance and metabolic homeostasis. As a commensal bacterium,
Clostridium sporogenes
has been implicated in modulating host energy homeostasis, albeit the underlying mechanism remains elusive. Therefore, this study aimed to investigate the impact of
C. sporogenes
supplementation on various physiological parameters, intestinal morphology, particularly adipose tissue accumulation, and glucolipid metabolism in mice. The findings reveal that mice supplemented with
C. sporogenes
for 6 weeks exhibited a notable increase in body weight, fat mass, adipocyte size, and serum triglyceride (TG) levels. Notably, the increased fat accumulation is observed despite consistent feed intake in treated mice. Mechanistically,
C. sporogenes
supplementation significantly improved the structure integrity of intestinal villi and enhanced energy absorption efficiency while reducing excretion of carbohydrates and fatty acids in feces. This was accompanied by upregulation of glucose and fatty acid transporter expression. Furthermore, supplementation with
C. sporogenes
promoted adipogenesis in both liver and adipose tissues, as evidenced by increased levels of hepatic pyruvate, acetyl-CoA, and TG, along with elevated expression levels of genes associated with lipid synthesis. Regarding the microbiological aspect,
C. sporogenes
supplementation correlated with an increased abundance of
Clostridium
genus bacteria and enhanced carbohydrate enzyme activity. In summary,
C. sporogenes
supplementation significantly promotes fat accumulation in mice by augmenting energy absorption and adipogenesis, possibly mediated by the expansion of
Clostridium
bacteria population with robust glycolipid metabolic ability.

IMPORTANCE

The
Clostridia
clusters have been implicated in energy metabolism, the specific species and underlying mechanisms remain unclear. This present study is the first to report
Clostridium sporogenes
is able to affect fat accumulation and glycolipid metabolism. We indicated that gavage of
C. sporogenes
promoted the adipogenesis and fat accumulation in mice by not only increasing the abundance of
Clostridium
bacteria but by also enhancing the metabolic absorption of carbohydrates and fatty acids significantly. Obviously, changes of gut microbiota caused by the
C. sporogenes
, especially the significant increase of
Clostridium
bacteria, contributed to the fat accumulation of mice. In addition, the enhancement of
Clostridium
genus bacteria remarkably improved the synthesis of hepatic pyruvate, acetyl-CoA, and triglyceride levels, as well as reduced the excretion of fecal carbohydrates, short-chain fatty acids, and free fatty acids remarkably. These findings will help us to understand the relationship of specific bacteria and host energy homeostasis.
Breast cancer symptom profile longitudinal changes: data mining study
Authors: Fathian Mohammad , Akbari Farzane 
Published: June 2024

ObjectivesIdentifying stable co-occurring symptoms in breast cancer (BC) patients during chemotherapy can improve symptom management and the treatment process. This study examines symptom cluster stability in Iranian BC patients receiving chemotherapy and evaluates stability across three-time points within each cluster.MethodsThis study collected data from three-time points: initial chemotherapy commencement, 2½ months postdiagnosis, and 5 months postdiagnosis. The research used exploratory factor analysis (EFA) in combination with hierarchical cluster analysis (HCA) and K means clustering to address research questions.ResultsIn the initial clustering step, EFA identified five clusters with high consistency across three-time points. The first cluster showed depression, anxiety and irritability, while the second cluster was characterised by sexual interest and pain. The third cluster was associated with diarrhoea and vomiting. In the second step, we obtained the HCA item output and two clusters of K means clustering that recorded depression and anxiety symptoms over time. Vomiting, dry mouth, sexual interest, worrying and numbness were observed during the first and second points, but the frequency has decreased since then.ConclusionsCancer’s psychological and physiological symptoms, including depression, anxiety, digestive and hormonal issues, remain stable throughout the disease. Palliative care centres can improve patients’ quality of life and treatment process by addressing persistent symptoms.
Opioid initiation timing and palliative care referrals in advanced cancer: retrospective study
Authors: Wong Aaron Kee Yee , Wang Dorothy , Gordon Ian , Alexander Marliese , Siew Beverly , Yap Natasha , Le Brian , Philip Jennifer 
Published: June 2024

ObjectivesEarly opioid initiation is recommended for advanced cancer pain, however the timing of opioid commencement in relation to diagnosis has not been described, and the role of palliative care prescribers is unclear. This study aims to determine the timing of opioid initiation by prescriber and cancer type in relation to key timepoints in the cancer illness course (diagnosis, palliative care referral and death).MethodsThis retrospective cohort study included patients at a quaternary cancer centre with incurable advanced cancer of five different subtype groups. Demographics, clinical characteristics, health service use and details of first slow and immediate release opioid prescription are reported.ResultsAmong 200 patients, median time to first immediate release opioid prescription was 23 days (IQR 1–82) and to slow release opioid prescription was 47 days (IQR 14–155). Most patients (95%, (n=190) were referred to palliative care (median time to referral 54 days (IQR 18–190)). Non-palliative care prescribers initiated slow release opioids for half the cohort (49%, n=97) prior to referral. Patients with pancreatic cancer had the shortest time to slow/immediate release opioid prescription (median 10 days (IQR 0–39) and 26 days (IQR 1–43) respectively) and shortest survival (median 136 days (IQR 82–214)).ConclusionsMedian time to opioid commencement was approximately 3 weeks after diagnosis. Despite early palliative care involvement, opioid initiation by non-palliative care clinicians was common and remains important. Timely palliative care referral for those with pancreatic cancer may include consideration of earlier complex pain presentations and shorter prognosis.