bluuebunny/crossref_metadata_2025_split huggingface dataset:
Species-level verification of
Phascolarctobacterium
association with colorectal cancer
Authors: Bucher-Johannessen Cecilie , Senthakumaran Thulasika , Avershina Ekaterina , Birkeland Einar , Hoff Geir , Bemanian Vahid , Tunsjø Hege , Rounge Trine B. 
Published: September 2024

ABSTRACT

We have previously demonstrated an association between increased abundance of
Phascolarctobacterium
and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the
Phascolarctobacterium
species, and their interaction with other microbial species. We analyze
Phascolarctobacterium
with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts—CRCAhus, NORCCAP, and CRCbiome—and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the
Phascolarctobacterium
pangenome. Three species of
Phascolarctobacterium
associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verified for
Phascolarctobacterium succinatutens
and negative associations were shown for
Phascolarctobacterium faecium
and adenoma in curatedMetagenomicData. Men show a higher prevalence of
P. succinatutens
across cohorts. Co-occurrence among
Phascolarctobacterium
species was low (<6%). Each of the three species shows distinct microbial composition and forms distinct correlation networks with other bacterial taxa, although
Dialister invisus
was negatively correlated to all investigated
Phascolarctobacterium
species. Pangenome analyses showed
P. succinatutens
to be enriched for genes related to porphyrin metabolism and degradation of complex carbohydrates, whereas glycoside hydrolase enzyme 3 was specific to
P. faecium
.

IMPORTANCE

Until now
Phascolarctobacterium
has been going under the radar as a CRC-associated genus despite having been noted, but overseen, as such for over a decade. We found not just one, but two species of
Phascolarctobacterium
to be associated with CRC—
Phascolarctobacterium succinatutens
was more abundant in adenoma/CRC, while
Phascolarctobacterium faecium
was less abundant in adenoma. Each of them represents distinct communities, constituted by specific microbial partners and metabolic capacities—and they rarely occur together in the same patients. We have verified that
P. succinatutens
is increased in adenoma and CRC and this species should be recognized among the most important CRC-associated bacteria.
Unraveling the benefits of
Bacillus subtilis
DSM 29784 poultry probiotic through its secreted metabolites: an
in vitro
approach
Authors: Vieco-Saiz Nuria , Prévéraud Damien P. , Pinloche Eric , Morat Aurélien , Govindin Pauline , Blottière Hervé M. , Matthieu Elliot , Devillard Estelle , Consuegra Jessika 
Published: September 2024

ABSTRACT

The probiotic
Bacillus subtilis
29784 (Bs29784) sustains chicken’s intestinal health, enhancing animal resilience and performance through the production of the bioactive metabolites hypoxanthine (HPX), niacin (NIA), and pantothenate (PTH). Here, using enterocyte
in vitro
models, we determine the functional link between these metabolites and the three pillars of intestinal resilience: immune response, intestinal barrier, and microbiota. We evaluated
in vitro
the capacity of Bs29784 vegetative cells, spores, and metabolites to modulate global immune regulators (using HT-29-NF-κB and HT-29-AP-1 reporter cells), intestinal integrity (HT-29-MUC2 reporter cells and Caco-2 cells), and cytokine production (Caco-2 cells). Finally, we simulated intestinal fermentations using chicken’s intestinal contents as inocula to determine the effect of Bs29784 metabolites on the microbiota and their fermentation profile. Bs29784 vegetative cells reduced the inflammatory response more effectively than spores, indicating that their benefit is linked to metabolic activity. To assess this hypothesis, we studied Bs29784 metabolites individually. The results showed that each metabolite had different beneficial effects. PTH and NIA reduced the activation of the pro-inflammatory pathways AP-1 and NF-κB. HPX upregulated mucin production by enhancing MUC2 expression. HPX, NIA, and PTH increased cell proliferation. PTH and HPX increased epithelial resilience to an inflammatory challenge by limiting permeability increase. In cecal fermentations, NIA increased acetate, HPX increased butyrate, whereas PTH increased acetate, butyrate, and propionate. In ileal fermentations, PTH increased butyrate. All molecules modulated microbiota, explaining the different fermentation patterns. Altogether, we show that Bs29784 influences intestinal health by acting on the three lines of resilience via its secreted metabolites.

IMPORTANCE

Probiotics provide beneficial metabolites to its host. Here, we describe the mode of action of a commonly used probiotic in poultry, Bs29784. By using
in vitro
cellular techniques and simulated chickens’ intestinal model, we show the functional link between Bs29784 metabolites and the three lines of animal resilience. Indeed, both Bs29784 vegetative cells and its metabolites stimulate cellular anti-inflammatory responses, strengthen intestinal barrier, and positively modulate microbiota composition and fermentative profile. Taken together, these results strengthen our understanding of the effect of Bs29784 on its host and explain, at least partly, its positive effects on animal health, resilience, and performance.
Geneticand phenotypic characterization of a novel ST45-K43 carbapenem-resistant
Klebsiella pneumoniae
strain causing bloodstream infection: a potential clinical threat
Authors: Chu Xiaobing , Jia Xinmiao , Jia Peiyao , Zhu Ying , Yu Wei , Liu Xiaoyu , Yang Qiwen 
Published: September 2024

ABSTRACT

Klebsiella pneumoniae
is a common pathogen of nosocomial infection, which can cause pneumonia, urinary tract infection, cystitis, and bloodstream infections (BSIs). Here, we genetically characterize a novel carbapenem-resistant
K. pneumoniae
(CRKP) strain recovered from the blood of a 44-year-old male patient with severe acute necrotizing pancreatitis and septic shock in China. The strain is a ST45
K. pneumoniae
with a novel serotype of K43, named 18SHX166. The susceptibility testing results showed that 18SHX166 was resistant to cephalosporin and carbapenems but still susceptible to ceftazidime-avibactam, quinolones, colistin, and amikacin. Genomic sequencing revealed that 18SHX166 contains three plasmids, namely pSHX166-Hv, pSHX166-KPC, and pSHX166-3. pSHX166-Hv harbored the
iucABCD
operon, encoding the siderophore of aerobactin. pSHX166-KPC harbored
bla
KPC-2
gene and possessed complete conjugative regions. The conjugation experiment verified pSHX166-KPC as a self-transmissible plasmid mediating the dissemination of antibiotic resistance, with a conjugation rate of 2.21 × 10
−5
. Additionally, the growth curve showed that 18SHX166 demonstrates a higher growth rate than the control strains. The characteristics of 18SHX166 indicate a potential high risk of clinical transmission.

IMPORTANCE

ST45-K43 carbapenem-resistant
Klebsiella pneumoniae
isolate, 18SHX166, carries a carbapenem resistance plasmid and virulence plasmid. It has the characteristics of multidrug resistance, high transmissibility, and a fast growth rate, which could pose a threat to the control of antimicrobial resistance and clinical transmission, causing a severe challenge to public health.
Antibiotic resistance plasmids in
Enterobacteriaceae
isolated from fresh produce in northern Germany
Authors: Stein Maria , Brinks Erik , Loop Jannike , Habermann Diana , Cho Gyu-Sung , Franz Charles M. A. P. 
Published: September 2024

ABSTRACT

In this study, the genomes of 22
Enterobacteriaceae
isolates from fresh produce and herbs obtained from retail markets in northern Germany were completely sequenced with MiSeq short-read and MinION long-read sequencing and assembled using a Unicycler hybrid assembly. The data showed that 17 of the strains harbored between one and five plasmids, whereas in five strains, only the circular chromosomal DNA was detected. In total, 38 plasmids were identified. The size of the plasmids detected varied between ca. 2,000 and 326,000 bp, and heavy metal resistance genes were found on seven (18.4%) of the plasmids. Eleven plasmids (28.9%) showed the presence of antibiotic resistance genes. Among large plasmids (>32,000 bp), IncF plasmids (specifically, IncFIB and IncFII) were the most abundant replicon types, while all small plasmids were Col-replicons. Six plasmids harbored unit and composite transposons carrying antibiotic resistance genes, with IS26 identified as the primary insertion sequence. Class 1 integrons carrying antibiotic resistance genes were also detected on chromosomes of two
Citrobacter
isolates and on four plasmids. Mob-suite analysis revealed that 36.8% of plasmids in this study were found to be conjugative, while 28.9% were identified as mobilizable. Overall, our study showed that
Enterobacteriaceae
from fresh produce possess antibiotic resistance genes on both chromosome and plasmid, some of which are considered to be transferable. This indicates the potential for
Enterobacteriaceae
from fresh produce that is usually eaten in the raw state to contribute to the transfer of resistance genes to bacteria of the human gastrointestinal system.

IMPORTANCE

This study showed that
Enterobacteriaceae
from raw vegetables carried plasmids ranging in size from 2,715 to 326,286 bp, of which about less than one-third carried antibiotic resistance genes encoding resistance toward antibiotics such as tetracyclines, aminoglycosides, fosfomycins, sulfonamides, quinolones, and β-lactam antibiotics. Some strains encoded multiple resistances, and some encoded extended-spectrum β-lactamases. The study highlights the potential of produce, which may be eaten raw, as a potential vehicle for the transfer of antibiotic-resistant bacteria.
Characterization of pKPN945B, a novel transferable IncR plasmid from hypervirulent carbapenem-resistant
Klebsiella pneumoniae
, harboring
bla
IMP-4
and
qnrS1
Authors: Xiao Xue , Feng Chunlin , Hao Jingchen , Cheng Ling , Jian Chunxia , Zeng Zhangrui , Liu Jinbo 
Published: September 2024

ABSTRACT

Carbapenem-resistant
Klebsiella pneumoniae
producing metallo-β-lactamase poses a major public health threat worldwide. Imipenemase often coexists with other resistance genes leading to the formation of multidrug-resistant bacteria. In this study, we describe the microbiological and genomic characteristics of the hypervirulent carbapenem-resistant
K. pneumoniae
ST20-K23 strain KPN945 harboring
bla
IMP-4
and
qnrS1
. The minimum inhibitory concentration of KPN945 against antimicrobials was determined by the broth microdilution method. The virulence of KPN945 was evaluated through string test, serum killing resistance, and
Galleria mellonella
larvae infection models. The transferability of pKPN945B was assessed using a conjugation test. The genome sequence characteristics of KPN945 were analyzed through whole genome sequencing, and a phylogenetic tree was constructed to evaluate the prevalence of imipenemase. Our findings showed that KPN945 was non-susceptible to β-lactam antibiotics, highly resistant to serum killing, and highly lethal to
G. mellonella
larvae. The fusion plasmid pKPN945B carried by the isolate KPN945 belonged to the IncR incompatibility group and harbored multiple drug resistance genes such as
bla
IMP-4
,
bla
CTX-M-14
,
qnrS1
, and
sul2
. The most important point is that the IncR plasmid is a novel plasmid that arose by the accretion of parts from different plasmids, making it transferable and with a fitness cost. Globally,
bla
IMP-4
is the most prevalent imipenemase subtype, with the highest isolation rates in Asia, particularly China. The spread of
bla
IMP-4
, especially the emergence of transferable plasmids, deserves our vigilance and prevention. Additionally, we should pay attention to the formation of hypervirulent
K. pneumoniae
mediated by non-virulent plasmids.

IMPORTANCE

Up to now, IncR replicons carrying
bla
IMP-4
have not been reported, and the IncR plasmids described in previous studies have been found to be non-transferrable to other bacteria through conjugation. Moreover, there have been no extensive phylogenetic analyses of strains carrying blaIMP in the published papers. The lack of data in these studies is noteworthy because blaIMP appears in the novel transferable fusion plasmid IncR. Although the IncR plasmid has no tra operon, it can still be transferred to
Escherichia coli
EC600 or
Klebsiella
pneumoniae ATCC13883 (RIF
R
) without high fitness cost, but it only affects the MIC of imipenem.
bla
IMP
integrates with other resistance mechanisms leading to the formation of multidrug-resistant strains. Notably, the high prevalence of
bla
IMP-4
in Asia and the presence of
bla
IMP-4
on novel transferable IncR plasmids suggest the urgent need to monitor the emergence of such plasmids and control their spread.
Methane-oxidizing bacterial community dynamics in sub-alpine forest soil
Authors: Beals Delaney G. , Munn J. Jackson , Puri Aaron W. 
Published: September 2024

ABSTRACT

Microbial activities in sub-alpine forest soil influence global cycling of the potent greenhouse gas methane. Understanding the dynamics of methane-oxidizing bacterial communities, particularly the roles of potentially active versus total microbial populations, is necessary for reducing uncertainty in global methane budget estimates. However, our understanding of the factors influencing methane cycling in forest soils is limited by our lack of knowledge about the biology of the microbes involved and how these communities are shaped by their environment. Here, we compared the composition and potential activity of microbial communities using 16S rRNA gene amplicon sequencing of total genomic DNA (gDNA) and potentially active complementary DNA (cDNA) from shallow soil in Red Butte Canyon (Salt Lake City, Utah, USA). We compared riparian and upland soils at two time points in the growing season and found distinct differences in both the community composition of the gDNA and cDNA libraries and the potential drivers of these community structures. Aerobic methane-oxidizing bacteria (methanotrophs) were detected in all samples, with cDNA libraries containing a higher average relative abundance and diversity of methanotrophs compared to gDNA libraries. Methane flux at the sample sites did not significantly correlate to the relative abundance (gDNA) or potential activity (cDNA) of methanotrophs. In the cDNA libraries, there were significant positive correlations between the abundance of
Methylococcaceae
family methanotrophs and several non-methanotrophic methylotrophs previously found to be associated with methane-oxidizing bacterial communities. These findings suggest a complex relationship between methane-cycling bacterial communities and methane flux and highlight the need for further
in situ
studies to understand the environmental and ecological influences of these microbial consortia.

IMPORTANCE
Methane-oxidizing bacteria are found in diverse soil and sediment environments and play an important role in mitigating flux of this potent greenhouse gas into the atmosphere. However, it is unclear how these bacteria and their associated communities are structured in the environment and how their activity ultimately influences methane flux. In this work, we examine the composition and structure of methane-oxidizing bacterial communities in sub-alpine forest soil and find soil- and time-specific differences between the stable and potentially active populations. We also find that the potentially active populations of certain methanotrophs and non-methanotrophs are positively correlated. This work provides a step toward refining our understanding of microbially mediated biogeochemical cycles.
PCR enables rapid detection of dermatophytes in practice
Authors: Aho-Laukkanen E. , Mäki-Koivisto V. , Torvikoski J. , Sinikumpu S. P. , Huilaja L. , Junttila I. S. 
Published: September 2024

ABSTRACT

Dermatophytes cause superficial infections of skin, hair, and nails. Even though they rarely cause severe infections, they are relatively common, particularly in primary health care. Diagnosis of dermatophyte infections has relied on relatively slow culture-based methods. Nucleic acid-based detection (PCR) methods might provide results more rapidly. Here, we describe the transition from culture-based methods into PCR-based methods in Northern Finland with a catchment area of approximately 720,000 mostly Caucasian people. This study included 14,330 samples collected between 2019 and 2022. Our results showed that the PCR-based method has become the diagnostic test of choice for these infections in this area. Commercial real-time PCR assay DermaGenius 2.0 complete multiplex test detected more positive results than culture and covered the most important dermatophytes,
Candida albicans
, and few less common species. With PCR, the mean turn-around-time from sample request to results decreased from 19 days to 16 hours.

IMPORTANCE
Superficial fungal infections, dermatophytosis, are remarkably common worldwide, affecting an estimated 20%–25% of the global population. In the diagnosis of these infections, fast and accurate results by PCR shorten the time to diagnosis and help clinicians to avoid unnecessary antifungal treatments.
Toward establishing a rapid constant temperature detection method for canine parvovirus based on endonuclease activities
Authors: Weng Shaoting , Ma Shengming , Xing Yueteng , Zhang Wenhui , Wu Yinrong , Fu Mengyao , Luo Zhongyi , Li Qiuying , Lin Sen , Zhang Longfei , Wang Yao 
Published: September 2024

ABSTRACT

Canine parvovirus (CPV) can cause high morbidity and mortality rates in puppies, posing a significant threat to both pet dogs and the breeding industry. Rapid, accurate, and convenient detection methods are important for the early intervention and treatment of canine parvovirus. In this study, we propose a visual CPV detection system called nucleic acid mismatch enzyme digestion (NMED). This system combines loop-mediated isothermal amplification (LAMP), endonuclease for gene mismatch detection, and colloidal gold lateral chromatography. We demonstrated that NMED can induce the binding of the amplicon from the sample to the specific labeling probe, which in turn triggers digestion by the endonuclease. The sensitivity and visual visibility of LAMP were increased by combining endonuclease and colloidal gold lateral chromatography assisted by a simple temperature-controlled device. The sensitivity of the NMED assay was 1 copy/μL, which was consistent with quantitative PCR (qPCR). The method was validated with 20 clinical samples that potentially had CPV infection; 15 positive samples and 5 negative samples were evaluated; and the detection accuracy was consistent with that of qPCR. As a rapid, accurate, and convenient molecular diagnostic method, NMED has great potential for application in the field of pathogenic microorganism detection.

IMPORTANCE
The NMED method has been established in the laboratory and used for CPV detection. The method has several advantages, including simple sampling, high sensitivity, intuitive results, and no requirement for expensive equipment. The establishment of this method has commercial potential and offers a novel approach and concept for the future development of clinical detection of pathogenic microorganisms.
Progressive inner retinal neurodegeneration in non-proliferative macular telangiectasia type 2
Authors: Amram Alec L , Whitmore S Scott , Wang Cheryl , Clavell Christine , Lyons Lance J , Rusakevich Alexander M , Han Ian , Folk James , Boldt H Culver , Stone Edwin M , Russell Stephen R , Lee Kyungmoo , Abramoff Michael , Wykoff Charles , Sohn Elliott H 
Published: September 2024

PurposePatients with non-proliferative macular telangiectasia type 2 (MacTel) have ganglion cell layer (GCL) and nerve fibre layer (NFL) loss, but it is unclear whether the thinning is progressive. We quantified the change in retinal layer thickness over time in MacTel with and without diabetes.MethodsIn this retrospective, multicentre, comparative case series, subjects with MacTel with at least two optical coherence tomographic (OCT) scans separated by >9 months OCTs were segmented using the Iowa Reference Algorithms. Mean NFL and GCL thickness was computed across the total area of the early treatment diabetic retinopathy study grid and for the inner temporal region to determine the rate of thinning over time. Mixed effects models were fit to each layer and region to determine retinal thinning for each sublayer over time.Results115 patients with MacTel were included; 57 patients (50%) had diabetes and 21 (18%) had a history of carbonic anhydrase inhibitor (CAI) treatment. MacTel patients with and without diabetes had similar rates of thinning. In patients without diabetes and untreated with CAIs, the temporal parafoveal NFL thinned at a rate of −0.25±0.09 µm/year (95% CI [−0.42 to –0.09]; p=0.003). The GCL in subfield 4 thinned faster in the eyes treated with CAI (−1.23±0.21 µm/year; 95% CI [−1.64 to –0.82]) than in untreated eyes (−0.19±0.16; 95% CI [−0.50, 0.11]; p<0.001), an effect also seen for the inner nuclear layer. Progressive outer retinal thinning was observed.ConclusionsPatients with MacTel sustain progressive inner retinal neurodegeneration similar to those with diabetes without diabetic retinopathy. Further research is needed to understand the consequences of retinal thinning in MacTel.
Management of atrial fibrillation in older adults
Authors: Parks Anna L , Frankel David S , Kim Dae H , Ko Darae , Kramer Daniel B , Lydston Melis , Fang Margaret C , Shah Sachin J 
Published: September 2024

Abstract
Most people with atrial fibrillation are older adults, in whom atrial fibrillation co-occurs with other chronic conditions, polypharmacy, and geriatric syndromes such as frailty. Yet most randomized controlled trials and expert guidelines use an age agnostic approach. Given the heterogeneity of aging, these data may not be universally applicable across the spectrum of older adults. This review synthesizes the available evidence and applies rigorous principles of aging science. After contextualizing the burden of comorbidities and geriatric syndromes in people with atrial fibrillation, it applies an aging focused approach to the pillars of atrial fibrillation management, describing screening for atrial fibrillation, lifestyle interventions, symptoms and complications, rate and rhythm control, coexisting heart failure, anticoagulation therapy, and left atrial appendage occlusion devices. Throughout, a framework is suggested that prioritizes patients’ goals and applies existing evidence to all older adults, whether atrial fibrillation is their sole condition, one among many, or a bystander at the end of life.