bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the utility of a rapid vesicle isolation method for clinical strains of
Pseudomonas aeruginosa
Authors: Henriquez Tania , Santoro Francesco , Medaglini Donata , Pallecchi Lucia , Clemente Ilaria , Bonechi Claudia , Magnani Agnese , Paccagnini Eugenio , Gentile Mariangela , Lupetti Pietro , Marvasi Massimiliano , Pini Alessandro , Bracci Luisa , Falciani Chiara 
Published: September 2024

ABSTRACT

Pseudomonas aeruginosa
, a pathogen capable of causing diseases ranging from mild to life-threatening, has a large arsenal of virulence factors. Notably, extracellular vesicles have emerged as significant players in the pathogenesis of this organism. However, the full range of their functions is still being studied, and difficulties related to vesicle purification (long protocols, low yields, and specialized instruments) have become a major obstacle for their characterization. In this context, the utility of rapid new methods of vesicle isolation from clinical strains is still unknown. Here, we analyze the utility of the ExoBacteria OMV isolation kit for a collection of clinical strains of
P. aeruginosa
. We first phenotypically characterized 15
P
.
aeruginosa
strains to ensure that our samples were heterogeneous. We then determined the best conditions for purifying vesicles from
P. aeruginosa
PAO1 reference strain by the rapid method and used them to isolate vesicles from clinical strains. Our results indicated that M9 minimal medium is the best for obtaining high purity with the rapid isolation kit. Although we were able to isolate vesicles from at least four strains, the low yield and the large number of strains with unpurifiable vesicles showed that the kit was not practical or convenient for clinical strains. Our findings suggest that although fast procedures for vesicle purification can be of great utility for
Escherichia coli
, the more complex phenotypes of clinical isolates of
P. aeruginosa
are a challenge for these protocols and new alternatives/optimizations need to be developed.

IMPORTANCE

Pseudomonas aeruginosa
is recognized as an opportunistic pathogen in humans and animals. It can effectively colonize various environments thanks to a large set of virulence factors that include extracellular vesicles. Different methods were recently developed to reduce the time and effort associated with vesicle purification. However, the utility of rapid vesicle isolation methods for clinical strains of
P. aeruginosa
(which are recognized as being highly diverse) is not yet known. In this context, we analyzed the utility of the ExoBacteria OMV Isolation kit for vesicle purification in
P. aeruginosa
clinical strains. Our findings showed that the kit does not seem to be convenient for research on clinical strains due to low vesicle recovery. Our results underscore the importance of developing new rapid vesicle purification protocols/techniques for specific clinical phenotypes.
Characterization of acquired β-lactamases in
Pseudomonas aeruginosa
and quantification of their contributions to resistance
Authors: Glen Karl A. , Lamont Iain L. 
Published: September 2024

ABSTRACT

Pseudomonas aeruginosa
is a highly problematic opportunistic pathogen that causes a range of different infections. Infections are commonly treated with β-lactam antibiotics, including cephalosporins, monobactams, penicillins, and carbapenems, with carbapenems regarded as antibiotics of last resort. Isolates of
P. aeruginosa
can contain horizontally acquired
bla
genes encoding β-lactamase enzymes, but the extent to which these contribute to β-lactam resistance in this species has not been systematically quantified. The overall aim of this research was to address this knowledge gap by quantifying the frequency of β-lactamase-encoding genes in
P. aeruginosa
and by determining the effects of β-lactamases on susceptibility of
P. aeruginosa
to β-lactams. Genome analysis showed that β-lactamase-encoding genes are present in 3% of
P. aeruginosa
but are enriched in carbapenem-resistant isolates (35%). To determine the substrate antibiotics, 10 β-lactamases were expressed from an integrative plasmid in the chromosome of
P. aeruginosa
reference strain PAO1. The β-lactamases reduced susceptibility to a variety of clinically used antibiotics, including carbapenems (meropenem, imipenem), penicillins (ticarcillin, piperacillin), cephalosporins (ceftazidime, cefepime), and a monobactam (aztreonam). Different enzymes acted on different β-lactams. β-lactamases encoded by the genomes of
P. aeruginosa
clinical isolates had similar effects to the enzymes expressed in strain PAO1. Genome engineering was used to delete β-lactamase-encoding genes from three carbapenem-resistant clinical isolates and increased susceptibility to substrate β-lactams. Our findings demonstrate that acquired β-lactamases play an important role in β-lactam resistance in
P. aeruginosa
, identifying substrate antibiotics for a range of enzymes and quantifying their contributions to resistance.

IMPORTANCE

Pseudomonas aeruginosa
is an extremely problematic pathogen, with isolates that are resistant to the carbapenem class of β-lactam antibiotics being in critical need of new therapies. Genes encoding β-lactamase enzymes that degrade β-lactam antibiotics can be present in
P. aeruginosa
, including carbapenem-resistant isolates. Here, we show that β-lactamase genes are over-represented in carbapenem-resistant isolates, indicating their key role in resistance. We also show that different β-lactamases alter susceptibility of
P. aeruginosa
to different β-lactam antibiotics and quantify the effects of selected enzymes on β-lactam susceptibility. This research significantly advances the understanding of the contributions of acquired β-lactamases to antibiotic resistance, including carbapenem resistance, in
P. aeruginosa
and by implication in other species. It has potential to expedite development of methods that use whole genome sequencing of infecting bacteria to inform antibiotic treatment, allowing more effective use of antibiotics, and facilitate the development of new antibiotics.
Changes in the pharyngeal and nasal microbiota in pediatric patients with adenotonsillar hypertrophy
Authors: Del Chierico Federica , Piazzesi Antonia , Fiscarelli Ersilia Vita , Ristori Maria Vittoria , Pirona Ilaria , Russo Alessandra , Citerà Nicoletta , Macari Gabriele , Santarsiero Sara , Bianco Fabrizio , Antenucci Valeria , Damiani Valerio , Mercuri Luigi , De Vincentis Giovanni Carlo , Putignani Lorenza 
Published: September 2024

ABSTRACT

The present study aimed to investigate the pharyngeal and nasal microbiota composition in children with adenotonsillar hypertrophy (AH) and assess longitudinal alterations in both microbiota after a probiotic oral spray treatment. A cohort of 57 AH patients were enrolled and randomly assigned to the probiotic and placebo groups for a 5-month treatment course. Pharyngeal and nasal swabs were collected before and after treatment and analyzed by 16S rRNA-based metataxonomics and axenic cultures for pathobiont identification. 16S rRNA sequences from pharyngeal and nasal swabs of 65 healthy children (HC) were used as microbiota reference profiles. We found that the pharyngeal and nasal microbiota of AH children were similar. When compared to HC, we observed an increase of the genera
Rothia
,
Granulicatella
,
Streptococcus
,
Neisseria
, and
Haemophilus
, as well as a reduction of
Corynebacterium
,
Pseudomonas, Acinetobacter,
and
Moraxella
in both microbiota of AH patients. After probiotic treatment, we confirmed the absence of adverse effects and a reduction of upper respiratory tract infections (URTI). Moreover, the composition of pharyngeal microbiota was positively influenced by the reduction of potential pathobionts, like
Haemophilus
spp., with an increase of beneficial microbial metabolic pathways. Finally, the probiotic reduced the abundance of the pathobionts
Streptococcus mitis
and
Gemella haemolysans
in relation to AH severity. In conclusion, our results highlight the alterations of the pharyngeal and nasal microbiota associated with AH. Moreover, probiotic administration conferred protection against URTI and reduced the presence of potential pathobionts in patients with AH.

IMPORTANCE
Adenotonsillar hypertrophy (AH) is considered the main cause of breathing disorders during sleep in children. AH patients, after significant morbidity and often multiple courses of antibiotics, often proceed to tonsillectomy and/or adenoidectomy. Given the potential risks associated with these procedures, there is a growing interest in the use of nonsurgical adjuvant therapies, such as probiotics, that could potentially reduce their need for surgical intervention. In this study, we investigated the pharyngeal and nasal microbiota in patients with AH compared with healthy children. Furthermore, we tested the effects of probiotic spray administration on both disease symptoms and microbiota profiles, to evaluate the possible use of this microbial therapy as an adjuvant for AH patients.
Dynamic response of the intestinal microbiome to
Eimeria maxima-
induced coccidiosis in chickens
Authors: Liu Jing , Guo Jiaqing , Whitmore Melanie A. , Tobin Isabel , Kim Dohyung M. , Zhao Zijun , Zhang Guolong 
Published: September 2024

ABSTRACT

Eimeria maxima
is a major cause of coccidiosis in chickens and a key predisposing factor for other economically significant diseases such as necrotic enteritis. However, a detailed understanding of the intestinal microbiome response to
E. maxima
infection is still lacking. This study aimed to comprehensively investigate the dynamic changes of the intestinal microbiome for 14 days post-infection (dpi) with
E. maxima
. Bacterial 16S rRNA gene sequencing was performed with the ileal and cecal digesta collected from mock and
E. maxima-
infected chickens at the prepatent (3 dpi), acute (5 and 7 dpi), and recovery phases (10 and 14 dpi) of infection. Although no notable changes were observed at 3 dpi, significant alterations of the microbiota occurred in both the ileum and cecum at 5 and 7 dpi. By 14 dpi, the intestinal microbiota tended to return to a healthy state. Notably,
Lactobacillus
was enriched in response to
E. maxima
infection in both the ileum and cecum, although individual
Lactobacillus
,
Ligilactobacillus
, and
Limosilactobacillus
species varied in the temporal pattern of response. Concurrently, major short-chain fatty acid-producing bacteria, such as
Faecalibacterium
, were progressively suppressed by
E. maxima
in the cecum. On the other hand, opportunistic pathogens such as
Escherichia
,
Enterococcus
, and
Staphylococcus
were significantly enriched in the ileum during acute infection.

IMPORTANCE

We have observed for the first time the dynamic response of the intestinal microbiota to
Eimeria maxima
infection, synchronized with its life cycle. Minimal changes occur in both the ileal and cecal microbiota during early infection, while significant alterations coincide with acute infection and disruption of the intestinal mucosal lining. As animals recover from coccidiosis, the intestinal microbiota largely returns to normal.
E. maxima
-induced intestinal inflammation likely creates an environment conducive to the growth of aerotolerant anaerobes such as
Lactobacillus
, as well as facultative anaerobes such as
Escherichia
,
Enterococcus
, and
Staphylococcus
, while suppressing the growth of obligate anaerobes such as short-chain fatty acid-producing bacteria. These findings expand our understanding of the temporal dynamics of the microbiota structure during
Eimeria
infection and offer insights into the pathogenesis of coccidiosis, supporting the rationale for microbiome-based strategies in the control and prevention of this condition.
Hepatitis B surface antigen impairs TLR4 signaling by upregulating A20 expression in monocytes
Authors: Wang Cong , Huang Chenlu , Li Yaming , Bai Jinjin , Zhao Kuangjie , Fang Zhong , Chen Jieliang 
Published: September 2024

ABSTRACT

Toll-like receptors (TLRs) play a crucial role in eliminating viral infection. Conversely, viruses have evolved various strategies to disrupt TLR signaling during chronic infection. In the case of hepatitis B virus (HBV), we previously reported that plasma hepatitis B surface antigen (HBsAg) is closely associated with impaired TLR responses in peripheral blood mononuclear cells from chronic hepatitis B (CHB) patients, but the reasons remain unclear. In this study, we investigated the mechanism by which HBsAg suppresses TLR4 signaling in monocyte cell lines. The monocyte cell line THP-1 was pretreated with HBsAg, followed by lipopolysaccharide (LPS) stimulation. Levels of proinflammatory cytokines and the activation of NF-κB, c-JNK, and ERK were examined. We found that HBsAg did not influence the LPS-induced activation of p65, but it disrupted NF-κB promoter activity through the ectopic expression of myeloid differentiation factor 88 (MyD88) and TAK1, suggesting that HBsAg can block downstream TLR4 signaling. Furthermore, we proved that LPS-induced polyubiquitination of tumor necrosis factor receptor-associated factor 6 (TRAF6) and the formation of the TRAF6-TAB2 complex were inhibited in HBsAg-pretreated cells. Interestingly, HBsAg led to a significant upregulation of A20, a ubiquitin-editing enzyme. Correspondingly, downregulation of A20 using siRNA restored LPS-mediated cytokines production, reflecting its crucial role in HBsAg-mediated inhibition of TLR4 signaling. These results demonstrated a novel mechanism by which HBsAg disrupts TLR4 signaling through the upregulation of A20, suggesting that targeting A20 may be a potential strategy to help restore monocyte functions.

IMPORTANCE
Clearance HBsAg indicates a functional cure of HBV infection, but in chronic hepatitis B (CHB), it is hard to achieve. HBsAg has been found to regulate anti-viral immune responses, such as the activation of TLR. Our previous jobs proved that HBsAg negatively correlates with TLR2/4 activation in monocytes from CHB patients and blocks TLR2 ligand-indcuced IL-12 production in monocytes. However, how TLR4 signaling is affected by HBsAg remains unknown. In this study, we not only observed impaired TLR4 activation after pretreated monocytes with HBsAg but also identified HBsAg-induced A20 play a role in this impairment, which suggests that targeting A20 may be a viable strategy to restore monocyte functions in CHB.
Descriptive and molecular epidemiology of leishmaniasis diagnosed from clinical samples in the United States, 2021-2022
Authors: Truong Thao T. , Crawford Karissa , Wang-McGuire Ichih , Jensen Kendal , Mushtaq Aisha , Lieberman Nicole A. P. , Buckner Frederick S. , Van Voorhis Wesley C. , Cookson Brad T. , Salipante Stephen J. , Lieberman Joshua A. 
Published: September 2024

ABSTRACT

Leishmaniasis is a rare disease in the United States, with an estimated annual incidence of dozens of cases occurring primarily in travelers, migrants, and military personnel. True disease incidence is unknown, since leishmaniasis is not a nationally notifiable condition. Here, we describe the results of molecular leishmaniasis over a 1-year interval (September 2021 to August 2022) when our laboratory served as the primary national reference laboratory for molecular diagnosis of civilian leishmaniasis. We tested 218 specimens submitted from 36 states yielding 94 of the 186 (50.5%) positive cases with species or species complex-level identification and 18 novel mini-exon alleles. Most species belonged to subgenus
Viannia
(75.6%) and associated with cutaneous or mucocutaneous disease. Cases were associated with recent travel (18.1%), travel timing unspecified (7.4%), migration (7.4%), remote travel (2.1%), military (1.1%), or unknown history (63.8%). These data illustrate the clinical utility of molecular testing for leishmaniasis and provide unique insight into disease epidemiology.

IMPORTANCE

Leishmaniasis is a disfiguring, neglected parasitic infection endemic to the Southern United States and the Americas. Despite significant populations at risk—travelers, military and foreign service members, and migrating persons—the epidemiology of the disease in the United States is poorly understood. Moreover, few clinical laboratories in the United States can test for the disease. Here, we present results from 1 year of testing for this disease at a major reference laboratory. These findings are particularly relevant because they coincide with a temporary “pause” on all clinical testing at the CDC. Our findings suggest at least several hundred cases occur each year in the United States. In particular, mucosal leishmaniasis may be more common than previously reported. We also highlight greater genetic diversity in
Leishmania
species endemic to the Americas than has been previously sampled, with implications for diagnostic specificity.
Enhanced Phase Stability and Reduced Bandgap for CsPbI3 Perovskite through Bi3+ and Cl– Co-Doping
Authors: Jiajia Zhang  
Published: September 2024

Abstract
All-inorganic perovskite CsPbI3 is emerging as a thermally more stable alternative to organic-inorganic hybrid perovskites. However, CsPbI3 perovskite suffers from poor phase stability at ambient temperature, and its bandgap is a bit too large as light-harvesting materials in both single-junction and perovskite-on-silicon tandem solar cells. In this study, we propose an electrically neutral co-doping strategy that equimolar Bi3+ (occupying the Pb site) and Cl– (occupying the interstitial site) are incorporated into CsPbI3. Unlike the individual Bi3+ or Cl– doping, the neutral co-doping can avoid stimulating the formation of the detrimental native defects. Our first-principles calculations suggest that the co-doped systems are stable at ambient temperature and possess narrower bandgaps compared with the undoped CsPbI3. Moreover, the electron and hole states are spatially separated in these multiple-ion compounds.
Impact Craters on Earth with a Diameter of More than 200 km: Numerical Modeling
Authors: Ivanov B. A. 
Published: September 2024

Abstract
The three largest impact craters, the remains of which have been found on Earth to date, had diameters of about 200 km immediately after formation. The search for traces of larger impact structures continues. This paper presents the results of numerical modeling of the formation of terrestrial impact craters larger than those already found. It is shown that the inferred geothermal gradient significantly influences the initial geometry of the impact melt region, which may facilitate the search for the remains of deeply eroded ancient impact structures.
Sustainability assessment of a quality improvement initiative on the management of bronchiolitis
Authors: Montejo Marta , Paniagua Natalia , Pijoan Jose Ignacio , Saiz-Hernando Carlos , Sanchez Alvaro , Rueda-Etzebarria Mikel , Benito Javier 
Published: September 2024

Background
A bronchiolitis integrated care pathway (BICP) achieved an 87% reduction in the use of medications in our regional health service (RHS) during the 2019–2020 season.

Aim
This study aimed to assess the sustainability of the changes in bronchiolitis management over 3 years after implementation of the BICP.

Methods
A prospective observational study on rates of medications prescribing in children diagnosed with bronchiolitis in 135 primary care (PC) centres and eight hospital emergency departments (EDs) in the Basque Country, Spain, was conducted during the four bronchiolitis seasons between 2019 and 2023. Over this period, the deployment of BICP-related actions continued in our RHS. In addition, a strategy was designed to enhance the sustainability of the results. The main endpoint was the percentage of children prescribed salbutamol.

Results
Over the 2019–2020 to 2022–2023 epidemic waves, 12 966 infants were diagnosed with bronchiolitis in PC, and 6676 infants in EDs. Rates of salbutamol use over the four waves were 5.04%, 10.54%, 8.51% and 6.05%, respectively, in PC and 3.36%, 10.02%, 7.62% and 5.77% in EDs. Rates of concomitant administration of other medications in EDs over the four waves were 3.2%, 0.2%, 1.0% and 1.9% for epinephrine and 0.4%, 0.7%, 0.3% and 0.4% for corticosteroids, respectively. In PC, prescribing rates were 5.1% and 1.8%, 10.3% and 4.1% for antibiotics and 7.8% and 4.5%, 5.7% and 2.5% for corticosteroids, respectively.

Conclusions
Reductions in the use of medications for bronchiolitis achieved in 2019 through the implementation of our integrated clinical pathway have been sustained over the three subsequent waves.
Impact of increasing workforce racial diversity on black-white disparities in cardiovascular disease mortality
Authors: Colbeth Hilary L , Riddell Corinne A , Thomas Marilyn , Mujahid Mahasin , Eisen Ellen A 
Published: September 2024

BackgroundStructural racism’s influence on workforce policies and practices presents possible upstream targets for assessing and reducing racial health disparities. This study is the first to examine workforce racial diversity in association with racial disparities in cardiovascular disease (CVD) outcomes.MethodsThis retrospective cohort study of 39 693 hourly autoworkers from three Michigan automobile plants, includes 75 years of follow-up (1941–2015). Workforce racial diversity (per cent black autoworkers) was a plant and year level variable. Annual exposure was cumulated over each individual’s working life and divided by time since hire. This time-varying measure was categorised into low, moderate and high. We estimated age-standardised rates of CVD and Cox proportional HRs by race.ResultsCVD mortality per 100 000 person-years decreased among autoworkers over the study period; however, black workers’ rates remained higher than white workers. Among black workers, we observed a strong protective association between greater workforce racial diversity and CVD mortality. For example, at the Detroit plant, the HR for moderate exposure to racial diversity was 0.94 (0.83, 1.08) and dropped to 0.78 (0.67, 0.90) at the highest level. Among white workers, results were mixed by plant, with protective effects in plants where less than 20% of workers were black and null results where black workers became the majority.ConclusionOur findings provide evidence that workplace racial diversity may reduce CVD mortality risk among black workers. Workplace practices encouraging diverse hiring and retention have potential to improve all workers’ health; particularly the socially racialised groups in that workforce.
The riverscape on a chip: high-throughput qPCR enables basin-wide fishery assessments
Authors: Elmore Joanna W. , Wilcox Taylor M. , Young Michael K. , Kopp Steve M. , Carim Kellie J. , Mason Daniel H. , Franklin Thomas W. , Schwartz Michael K. 
Published: September 2024

To achieve reliable detection of environmental DNA (eDNA) from multiple species, a method which combines the specificity of single-taxon assays with the broad taxonomic coverage of metabarcoding is needed. High-throughput quantitative PCR (HT-qPCR) has emerged as one such method that holds particular promise for ecological applications. Here, we present the development and validation of a HT-qPCR biochip (i.e., biochip) protocol for a suite of western North American fishes with high cultural, economic, and ecological significance. Coupling this biochip with systematically distributed eDNA samples collected by citizen scientists, we evaluated the distribution of multiple species throughout a large river basin in the U.S. Pacific Northwest. Patterns of detection using the biochip were comparable to those using single-taxon qPCR (ST-qPCR; mean concordance = 0.917), despite the biochip using 90% less DNA per taxon and reducing costs by an estimated 40%. Comparisons between biochip results and distributions derived from conventional methods demonstrate that this approach not only offers more reliable and high-resolution distribution data for these species but also achieves this more efficiently than traditional sampling methods.