bluuebunny/crossref_metadata_2025 huggingface dataset:
A systematic review of the application of machine learning techniques to ultrasound tongue imaging analysis
Authors: Xia Zhen , Yuan Ruicheng , Cao Yuan , Sun Tao , Xiong Yunsheng , Xu Kele
Published: September 2024

B-mode ultrasound has emerged as a prevalent tool for observing tongue motion in speech production, gaining traction in speech therapy applications. However, the effective analysis of ultrasound tongue image frame sequences (UTIFs) encounters many challenges, such as the presence of high levels of speckle noise and obscured views. Recently, the application of machine learning, especially deep learning techniques, to UTIF interpretation has shown promise in overcoming these hurdles. This paper presents a thorough examination of the existing literature, focusing on UTIF analysis. The scope of our work encompasses four key areas: a foundational introduction to deep learning principles, an exploration of motion tracking methodologies, a discussion of feature extraction techniques, and an examination of cross-modality mapping. The paper concludes with a detailed discussion of insights gleaned from the comprehensive literature review, outlining potential trends and challenges that lie ahead in the field.
The role of signaling pathways mediated by the GPCRs CysLTR1/2 in melanocyte proliferation and senescence
Authors: Huber Thomas , Horioka-Duplix Mizuho , Chen Yuanhuang , Saca Victoria R. , Ceraudo Emilie , Chen Yu , Sakmar Thomas P.
Published: September 2024

In contrast with sun exposure–induced melanoma, rarer melanocytic tumors and neoplasms with low mutational burden present opportunities to study isolated signaling mechanisms. These include uveal melanoma and blue nevi, which are often driven by mutations within the G protein–coupled signaling cascade downstream of cysteinyl leukotriene receptor 2. Here, we review how the same mutations within this pathway drive the growth of melanocytes in one tissue but can inhibit the growth of those in another, exemplifying the role of the tissue environment in the delicate balance between uncontrolled cell growth and senescence.
Suppressing appetite with taurine
Authors: VanHook Annalisa M.
Published: September 2024

The taurine metabolite
N
-acetyltaurine protects mice from diet-induced obesity by reducing food intake.
In vivo
and
in vitro
analyses of the role of the Prc protease in inducing mucoidy in
Pseudomonas aeruginosa
Authors: Sommerfield Alexis G. , Wang Michelle , Mamana Julia , Darwin Andrew J.
Published: September 2024

In
Pseudomonas aeruginosa
, alginate biosynthesis gene expression is inhibited by the transmembrane anti-sigma factor MucA, which sequesters the AlgU sigma factor. Cell envelope stress initiates cleavage of the MucA periplasmic domain by site-1 protease AlgW, followed by further MucA degradation to release AlgU. However, after colonizing the lungs of people with cystic fibrosis,
P. aeruginosa
converts to a mucoid form that produces alginate constitutively. Mucoid isolates often have
mucA
mutations, with the most common being
mucA22
, which truncates the periplasmic domain. MucA22 is degraded constitutively, and genetic studies suggested that the Prc protease is responsible. Some studies also suggested that Prc contributes to induction in strains with wild-type MucA, whereas others suggested the opposite. However, missing from all previous studies is a demonstration that Prc cleaves any protein directly, which leaves open the possibility that the effect of a
prc
null mutation is indirect. To address the ambiguities and shortfalls, we reevaluated the roles of AlgW and Prc as MucA and MucA22 site-1 proteases.
In vivo
analyses using three different assays and two different inducing conditions all suggested that AlgW is the only site-1 protease for wild-type MucA in any condition. In contrast, genetics suggested that AlgW or Prc act as MucA22 site-1 proteases in inducing conditions, whereas Prc is the only MucA22 site-1 protease in non-inducing conditions. For the first time, we also show that Prc is unable to degrade the periplasmic domain of wild-type MucA but does degrade the mutated periplasmic domain of MucA22 directly.

IMPORTANCE

After colonizing the lungs of individuals with cystic fibrosis,
Pseudomonas aeruginosa
undergoes mutagenic conversion to a mucoid form, worsening the prognosis. Most mucoid isolates have a truncated negative regulatory protein MucA, which leads to constitutive production of the extracellular polysaccharide alginate. The protease Prc has been implicated, but not shown, to degrade the most common MucA variant, MucA22, to trigger alginate production. This work provides the first demonstration that the molecular mechanism of Prc involvement is direct degradation of the MucA22 periplasmic domain and perhaps other truncated MucA variants as well. MucA truncation and degradation by Prc might be the predominant mechanism of mucoid conversion in cystic fibrosis infections, suggesting that Prc activity could be a useful therapeutic target.
Regulation of bacterial virulence genes by PecS family transcription factors
Authors: Nwokocha George C. , Ghosh Arpita , Grove Anne
Published: September 2024

Bacterial plant pathogens adjust their gene expression programs in response to environmental signals and host-derived compounds. This ensures that virulence genes or genes encoding proteins, which promote bacterial fitness in a host environment, are expressed only when needed. Such regulation is in the purview of transcription factors, many of which belong to the ubiquitous multiple antibiotic resistance regulator (MarR) protein family. PecS proteins constitute a subset of this large protein family. PecS has likely been distributed by horizontal gene transfer, along with the divergently encoded efflux pump PecM, suggesting its integration into existing gene regulatory networks. Here, we discuss the roles of PecS in the regulation of genes associated with virulence and fitness of bacterial plant pathogens. A comparison of phenotypes and differential gene expression associated with the disruption of
pecS
shows that functional consequences of PecS integration into existing transcriptional networks are highly variable, resulting in distinct PecS regulons. Although PecS universally binds to the
pecS-pecM
intergenic region to repress the expression of both genes, binding modes differ. A particularly relaxed sequence preference appears to apply for
Dickeya dadantii
PecS, perhaps to optimize its integration as a global regulator and regulate genes ancestral to the acquisition of
pecS-pecM
. Even inducing ligands for PecS are not universally conserved. It appears that PecS function has been optimized to match the unique regulatory needs of individual bacterial species and that its roles must be appreciated in the context of the regulatory networks into which it was recruited.
hnRNP H controls alternative splicing of human papillomavirus type 16 E1, E6, E7, and E6^E7 mRNAs via GGG motifs
Authors: Jönsson Johanna , Zhai Qiaoli , Schwartz Stefan , Kajitani Naoko
Published: September 2024

The mRNAs encoding the human papillomavirus type 16 (HPV16) E6 and E7 oncogene mRNAs are subjected to extensive alternative RNA splicing at multiple regulated splice sites. One of the most extensively used 5ʹ-splice sites in the HPV16 genome is named SD880 and is located immediately downstream of the E7 open reading frame. Here, we show that a cluster of three GGG-motifs adjacent to HPV16 SD880 interacts with heterogeneous nuclear ribonucleoprotein (hnRNP) H that cooperates with SD880 to stimulate splicing to the upstream HPV16 3’-splice site SA742. This splice site is located in the E7 coding region and is required for the production of the HPV16 226^742 mRNA that encodes the E6^E7 fusion protein. Enhancement of HPV16 E6^E7 mRNA production by hnRNP H occurred at the expense of the intron-retained E6 mRNAs and the spliced E7 mRNAs, demonstrating that hnRNP H controls the relative levels of E6, E7, and E6^E7 proteins. Unexpectedly, overexpression of hnRNP H also promoted retention of the downstream E1 encoding intron and enhanced E1 protein production. We concluded that hnRNP H plays an important role in the HPV16 gene expression program.

IMPORTANCE

Here, we show that hnRNP H binds to multiple GGG-motifs downstream of human papillomavirus type 16 (HPV16) splice site SD880 and acts in concert with SD880 to promote expression of the HPV16 E6^E7 mRNA. The E6^E7 protein has been shown previously to stabilize the HPV16 E6 and E7 oncoproteins and may as such contribute to the carcinogenic properties of HPV16. In its capacity of major regulator of HPV16 oncogene expression, hnRNP H may be exploited as a target for antiviral drugs to HPV16.
Vascular endothelial growth factor receptor 2 as a potential host target for the inhibition of enterovirus replication
Authors: Zhao Xiaoyu , Qiao Rui , Hao Meng , Xu Longfa , Wang Dong , Lu Yinying , Li Jiayan , Wu Jing , Li Yi , Cheng Tong , Zhang Wenhong , Zhao Jincun , Wang Pengfei
Published: September 2024

Because host kinases are key regulators of multiple signaling pathways in response to viral infections, we previously screened a kinase inhibitor library using rhabdomyosarcoma cells and human intestinal organoids in parallel to identify potent inhibitors against EV-A71 infection. We found that Rho-associated coiled-coil-containing protein kinase (Rock) inhibitor efficiently suppressed the EV-A71 replication and further revealed Rock1 as a novel EV-A71 host factor. In this study, subsequent analysis found that a variety of vascular endothelial growth factor receptor (VEGFR) inhibitors also had potent antiviral effects. Among the hits, Pazopanib, with a selectivity index as high as 254, which was even higher than that of Pirodavir, a potent broad-spectrum picornavirus inhibitor targeting viral capsid protein VP1, was selected for further analysis. We demonstrated that Pazopanib not only efficiently suppressed the replication of EV-A71 in a dose-dependent manner, but also exhibited broad-spectrum anti-enterovirus activity. Mechanistically, Pazopanib probably induces alterations in host cells, thereby impeding viral genome replication and transcription. Notably, VEGFR2 knockdown and overexpression suppressed and facilitated EV-A71 replication, respectively, indicating that VEGFR2 is a novel host dependency factor for EV-A71 replication. Transcriptome analysis further proved that VEGFR2 potentially plays a crucial role in combating EV-A71 infection through the TSAd-Src-PI3K-Akt pathway. These findings expand the range of potential antiviral candidates of anti-enterovirus therapeutics and suggest that VEGFR2 may be a key host factor involved in EV-A71 replication, making it a potential target for the development of anti-enterovirus therapeutics.

IMPORTANCE

As the first clinical case was identified in the United States, EV-A71, a significant neurotropic enterovirus, has been a common cause of hand, foot, and mouth disease (HFMD) in infants and young children. Developing an effective antiviral agent for EV-A71 and other human enteroviruses is crucial, as these viral pathogens consistently cause outbreaks in humans. In this study, we demonstrated that multiple inhibitors against VEGFRs effectively reduced EV-A71 replication, with Pazopanib emerging as the top candidate. Furthermore, Pazopanib also attenuated the replication of other enteroviruses, including CVA10, CVB1, EV-D70, and HRV-A, displaying broad-spectrum anti-enterovirus activity. Given that Pazopanib targets various VEGFRs, we narrowed the focus to VEGFR2 using knockdown and overexpression experiments. Transcriptomic analysis suggests that Pazopanib's potential downstream targets involve the TSAd-Src-PI3K-Akt pathway. Our work may contribute to identifying targets for antiviral inhibitors and advancing treatments for human enterovirus infections.
Identification of novel genetic factors that regulate c-di-AMP production in
Staphylococcus aureus
using a riboswitch-based biosensor
Authors: Kviatkovski Igor , Zhong Qiyun , Vaidya Sanika , Gründling Angelika
Published: September 2024

Nucleotide secondary messengers regulate various processes in bacteria allowing them to rapidly respond to changes in environmental conditions. c-di-AMP is an essential second messenger required for the growth of the human pathogen
Staphylococcus aureus
, regulating potassium, osmolyte uptake, and beta-lactam resistance. Cellular concentrations of c-di-AMP are regulated by the activities of two enzymes, DacA and GdpP, which synthesize and hydrolyze c-di-AMP, respectively. Besides these, only a limited number of other factors are known to regulate c-di-AMP levels. Using a c-di-AMP biosensor consisting of the
Bacillus subtilis
c-di-AMP-binding
kimA
riboswitch and
yfp,
we were able to efficiently detect differences in cellular c-di-AMP levels in
S. aureus
. To identify novel factors that regulate c-di-AMP levels, we introduced the biosensor into a library of
S. aureus
transposon mutants. In this manner, we obtained mutants with increased c-di-AMP levels that contained insertions in
gdpP
coding for the c-di-AMP hydrolase and
ybbR
(
cdaR
) coding for a c-di-AMP cyclase regulator, thus validating our screen. We also identified two high c-di-AMP mutants with insertions upstream of the
nrdIEF
operon coding for the ribonucleotide reductase enzyme. Further analysis revealed that the insertion down-regulated
nrdIEF
expression, indicating that the enzyme is a negative regulator of c-di-AMP production. This negative regulation was dependent on
rsh
, encoding for the synthase of the endogenous GdpP inhibitor (p)ppGpp. The methods established in this work can be readily adapted for use in other bacteria to uncover genetic or environmental factors regulating c-di-AMP levels.

IMPORTANCE

c-di-AMP is an important secondary messenger, produced by many bacterial species including the opportunistic pathogen
Staphylococcus aureus
. In this bacterium, c-di-AMP controls cell wall homeostasis, cell size, and osmotic balance. In addition, it has been shown that strains with high c-di-AMP levels exhibit increased resistance to beta-lactam antibiotics. Here, we developed a biosensor-based method for the rapid detection of c-di-AMP levels in
S. aureus
. We utilized the biosensor in a genetic screen for the identification of novel factors that impact cellular c-di-AMP. In this manner, we identified the ribonucleotide reductase as a novel factor altering cellular c-di-AMP levels and showed that reducing its expression leads to increased cellular c-di-AMP levels. As methicillin-resistant
S. aureus
strains are considered as a global health threat, it is important to study processes that dictate cellular c-di-AMP levels, which are associated with antibiotic resistance.
Differential immunological responses in lamb rumen and colon to alfalfa hay and wheat straw in a concentrate-rich diet: insights into microbe-host interactions
Authors: Gebeyew Kefyalew , Mi Hui , Liu Yong , Liu Yongbin , Wang Biao , Feyera Teka , Zhiliang Tan , He Zhixiong
Published: September 2024

The impact of a concentrate-rich (CR) diet on the gut microbiome and epithelium homeostasis is well documented. However, it has not been systematically studied whether and how host-microbial interaction contributes to the immune homeostasis in the rumen and colon of lambs fed alfalfa hay and wheat straw, alone or combined, in a CR diet. In all, 63 lambs (initial body weight, 16.69 ± 1.50 kg) were randomly allotted to three dietary groups, each consisting of three pens with seven lambs per pen. Over 14 weeks, the lambs were fed diets as follows: 60% concentrate supplemented with either 40% wheat straw (WG), 20% alfalfa hay combined with 20% wheat straw (MG), or 40% alfalfa hay (AG). The present findings showed that lambs in the AG group had greater (
P
< 0.05) IgG and lower (
P
= 0.067) tumor necrosis factor-alpha concentrations relative to those in the MG and WG groups. The 16S rRNA analysis highlighted that various bacterial phyla and genera in the rumen and colon preferentially degrade fiber and starch derived from alfalfa hay and wheat straw. The weighted gene co-expression network analysis revealed that the bacterial genera from the
Firmicutes
are broadly associated with genes involved in various signaling pathways, underscoring the potential role of
Firmicutes
as key drivers of host-microbial interactions under the present feeding conditions. These findings shed light on the fact that the rumen and colon immune homeostasis is distinctively influenced by diets of alfalfa hay, wheat straw, or their combination in a CR diet. Further studies should examine the prolonged effects of replacing wheat straw with alfalfa hay in a concentrate-rich diet formulated to provide equivalent neutral detergent fiber levels. This could reveal how various forage fibers influence host-microbial interactions and gut health.

IMPORTANCE

In contemporary feedlots, a growing trend is to feed animals a concentrate-rich (CR) diet that could disrupt the synchronized interplay between microbes and host metabolism, leading to altered metabolic functions. Wheat straw and alfalfa hay have different levels of protein and neutral detergent fiber, each with varying rates of digestion. It is unclear how including alfalfa hay and wheat straw, alone or combined in a CR diet, influences the host-microbial consortia and immune homeostasis. Herein, we showed that rumen and colon showed differential immune responses to the alfalfa hay, wheat straw, or both. Bacterial genera preferentially degrade fiber and starch derived from alfalfa hay, wheat straw, or both. Bacterial genera from
Firmicutes
phylum play a pivotal role in driving the host-microbial interactions, as indicated by their extensive association with genes across various signaling pathways.
Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes
Authors: Rappaport H. B. , Senewiratne Nimshika P. J. , Lucas Sarah K. , Wolfe Benjamin E. , Oliverio Angela M.
Published: September 2024

While research on the sourdough microbiome has primarily focused on lactic acid bacteria (LAB) and yeast, recent studies have found that acetic acid bacteria (AAB) are also common members. However, the ecology, genomic diversity, and functional contributions of AAB in sourdough remain unknown. To address this gap, we sequenced 29 AAB genomes, including three that represent putatively novel species, from a collection of over 500 sourdough starters surveyed globally from community scientists. We found variations in metabolic traits related to carbohydrate utilization, nitrogen metabolism, and alcohol production, as well as in genes related to mobile elements and defense mechanisms. Sourdough AAB genomes did not cluster when compared to AAB isolated from other environments, although a subset of gene functions was enriched in sourdough isolates. The lack of a sourdough-specific genomic cluster may reflect the nomadic lifestyle of AAB. To assess the consequences of AAB on the emergent function of sourdough starter microbiomes, we constructed synthetic starter microbiomes, varying only the AAB strain included. All AAB strains increased the acidification of synthetic sourdough starters relative to yeast and LAB by 18.5% on average. Different strains of AAB had distinct effects on the profile of synthetic starter volatiles. Taken together, our results begin to define the ways in which AAB shape emergent properties of sourdough and suggest that differences in gene content resulting from intraspecies diversification can have community-wide consequences on emergent function.

IMPORTANCE

This study is a comprehensive genomic and ecological survey of acetic acid bacteria (AAB) isolated from sourdough starters. By combining comparative genomics with manipulative experiments using synthetic microbiomes, we demonstrate that even strains with >97% average nucleotide identity can shift important microbiome functions, underscoring the importance of species and strain diversity in microbial systems. We also demonstrate the utility of sourdough starters as a model system to understand the consequences of genomic diversity at the strain and species level on multispecies communities. These results are also relevant to industrial and home-bakers as we uncover the importance of AAB in shaping properties of sourdough starters that have direct impacts on sensory notes and the quality of sourdough bread.
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

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

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

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

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

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

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

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

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

Purpose

Patients 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.

Methods

In 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.

Results

115 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.

Conclusions

Patients 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

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.
Neuroendocrine tumours found at endoscopy: diagnosis and staging
Authors: Khan Mohid S , Srirajaskanthan Raj , Frydman Aviva , Pritchard D Mark
Published: September 2024

Due to their increasing incidence, neuroendocrine neoplasms (NENs) are being detected more frequently by endoscopists while they are performing diagnostic upper or lower gastrointestinal (GI) endoscopies. These procedures are usually performed for unrelated indications or for screening, with the tumours often being detected incidentally. The most common scenario is of an endoscopist being surprised by receiving a histology report of a well-differentiated neuroendocrine tumour (NET) after biopsying a small polyp that was initially thought to be benign. This article aims to provide some guidance about what to do next in that situation. All patients with NET should, however, be referred to a fully constituted NEN multidisciplinary team for definitive investigations and management.

In general, the site, size and number of any possible NENs should be fully assessed during the initial endoscopy and representative endoscopic images should be captured. If the initial endoscopic assessment was inadequate, the procedure may need to be repeated. Possible NENs should be sampled using biopsy forceps. Endoscopic resection should only be attempted following histological confirmation of the diagnosis and tumour grade and after additional investigations have been performed to fully stage the tumour and determine its hormone production status. This is essential so that patients do not undergo either unnecessary or inadequate endoscopic resections.

This article discusses the endoscopic features and subsequent assessment of NENs that arise in the stomach, duodenum, terminal ileum and rectum, as these are the common tumour sites within the GI tract.
Neuropsychiatric symptoms in cognitive decline and Alzheimer’s disease: biomarker discovery using plasma proteomics
Authors: Rabl Miriam , Clark Christopher , Dayon Loïc , Popp Julius
Published: September 2024

Background and objectives

Neuropsychiatric symptoms (NPS) are common in older people with cognitive impairment and Alzheimer’s disease (AD). No biomarkers to detect the related pathology or predict the clinical evolution of NPS are available yet. This study aimed to identify plasma proteins that may serve as biomarkers for NPS and NPS-related clinical disease progression.

Methods

A panel of 190 plasma proteins was quantified using Luminex xMAP in the Alzheimer’s Disease Neuroimaging Initiative cohort. NPS and cognitive performance were assessed at baseline and after 1 and 2 years. Logistic regression, receiver operating characteristic analysis and cross-validation were used to address the relations of interest.

Results

A total of 507 participants with mild cognitive impairment (n=396) or mild AD dementia (n=111) were considered. Selected plasma proteins improved the prediction of NPS (area under the curve (AUC) from 0.61 to 0.76, p<0.001) and future NPS (AUC from 0.63 to 0.80, p<0.001) when added to a reference model. Distinct protein panels were identified for single symptoms. Among the selected proteins, ANGT, CCL1 and IL3 were associated with NPS at all three time points while CCL1, serum glutamic oxaloacetic transaminase and complement factor H were also associated with cognitive decline. The associations were independent of the presence of cerebral AD pathology as assessed using cerebrospinal fluid biomarkers.

Conclusions

Plasma proteins are associated with NPS and improve prediction of future NPS.
Genetic testing in dementia
Authors: O'Connor Antoinette , Ryan Natalie S , Belder Christopher R S , Lynch David S , Lahiri Nayana , Houlden Henry , Rohrer Jonathan D , Fox Nick C , O'Dowd Sean
Published: September 2024

There is growing public awareness and concern regarding dementia risk. In addition, genetic testing is increasingly accessible and is at the point of being integrated into routine clinical practice. As a result, there is a pressing need for treating clinicians to have the appropriate knowledge base to request and consent for diagnostic genetic testing in cognitive clinics. We outline our approach to genetic testing in patients with Alzheimer’s disease, frontotemporal dementia, dementia with Lewy bodies and vascular cognitive impairment. We discuss when to consider testing, the consenting process, and the interpretation and communication of genetic test results.