bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of the combination of amphotericin B and echinocandins against
Candida auris in vitro
and in the
Caenorhabditis elegans
host model
Authors: Hernando-Ortiz Ainara , Eraso Elena , Jauregizar Nerea , de Groot Piet W.J. , Quindós Guillermo , Mateo Estibaliz 
Published: November 2023

ABSTRACT

The multidrug-resistant
Candida auris
is a global health emergency, being responsible for outbreaks of invasive candidiasis worldwide. Limited effective therapeutic options make it difficult to treat this emerging pathogen. In this context, combinations of different antifungal drugs are considered a promising therapeutic alternative. The aim of this work was to analyze the antifungal activity of combinations of amphotericin B and echinocandins against five clinical blood isolates of
C. auris
. One of these isolates showed an aggregative phenotype already described in
C. auris
species, forming large aggregates of cells that are very difficult to disintegrate. First, the
in vitro
activity of these drugs was evaluated both in monotherapy and in combination, and results showed synergistic interactions between amphotericin B and echinocandins in most cases, although higher minimum inhibitory concentration (MIC) values were observed against the aggregative isolate compared to non-aggregative counterparts. The most promising drug combinations were then selected for
in vivo
activity evaluation using a
Caenorhabditis elegans
model of candidiasis and by determination of survival rates. The combination of amphotericin B and caspofungin showed the strongest protective effect during
C. elegans
infection with
C. auris
blood isolates, achieving up to 99%
C
.
elegans
survival. Although the MIC values for micafungin were low
in vitro
, these drug concentrations had no effect
in vivo
, and the combination of amphotericin B and micafungin was the least effective. The results of this study showed that the combination amphotericin B and echinocandins might be a promising therapeutic approach for the treatment of invasive candidiasis caused by
C. auris
. Moreover, the nematode
C. elegans
is a suitable alternative model for screening of new therapeutic agents capable of overcoming multidrug-resistant
C. auris
infections.

IMPORTANCE

Multidrug resistance is a rising problem among non-
Candida albicans
species, such as
Candida auris
. This therapeutic problem has been very important during the COVID-19 pandemic. The World Health Organization has included
C. auris
in its global priority list of health-threatening fungi, to study this emerging multidrug-resistant species and to develop effective alternative therapies. In the present study, the synergistic effect of the combination of amphotericin B and echinocandins has been demonstrated against blood isolates of
C. auris
. Different susceptibility responses were also observed between aggregative and non-aggregative phenotypes. The antifungal activity of these drug combinations against
C. auris
was also demonstrated in the
Caenorhabditis elegans
host model of candidiasis, confirming the suitability and usefulness of this model in the search for solutions to antimicrobial resistance.
Detection and absolute quantification of
Lactiplantibacillus plantarum
ATCC 202195 by quantitative real-time PCR
Authors: Shawon Jakaria , Pell Lisa G. , Kabir Mamun , Evans Kara , Hasan Mehedi , Li Grace , Qamar Huma , Starke Cody W. E. , Kurukulasuriya Shakya , Al Mahmud Abdullah , Sherman Philip M. , Sarker Shafiqul Alam , Roth Daniel E. , Haque Rashidul 
Published: November 2023

ABSTRACT

Lactiplantibacillus plantarum
ATCC 202195 has probiotic properties that may be beneficial in early infancy. Since the effects of probiotics are often strain and dose specific, tools are needed to identify and enumerate
L. plantarum
ATCC 202195 with high sensitivity and specificity. Herein, a probe-based real-time quantitative PCR (qPCR) assay was developed to detect and enumerate
L. plantarum
ATCC 202195. The probe sequence contained a single nucleotide polymorphism within gene FEE41_08190 that was unique to
L. plantarum
ATCC 202195 at the time of the assay’s design. The linear dynamic range of the assay spanned five orders of magnitude with an
R
2
that did not deviate from linearity and an amplification efficiency that ranged from 97% to 110% across six independent plates. At 95% confidence, the limit of detection in the assay was estimated at roughly 15 cells. No amplification was observed for reactions containing gDNA from seven other
Lactobacillus
species. This is the first report of a qPCR assay that detects and quantifies
L. plantarum
ATCC 202195. The assay is intended to be used as a resource for future clinical trials and commercial manufacturing settings.

IMPORTANCE

When administered for seven consecutive days shortly after birth, the probiotic bacterium
Lactiplantibacillus plantarum
ATCC 202195 plus fructooligosaccharide (FOS) was reported to reduce sepsis and lower respiratory tract infection events during early infancy in a randomized trial in India. Since probiotic effects are often strain specific, strain-level detection and quantification by routine molecular methods enables the monitoring of safety outcomes, such as probiotic-associated bacteremia, and allows for the quality of probiotic interventions to be assessed and monitored (i.e., verify strain identity and enumerate). Despite the potential clinical applications of
L. plantarum
ATCC 202195, an assay to detect and quantify this strain has not previously been described. Herein, we report the design of primer and probe sequences to detect
L. plantarum
ATCC 202195 and the development and optimization of a real-time PCR assay to detect and quantify the strain with high specificity and high sensitivity.
Co-PATHOgenex web application for assessing complex stress responses in pathogenic bacteria
Authors: Fernandez Leyden , Rosvall Martin , Normark Johan , Fällman Maria , Avican Kemal 
Published: November 2023

ABSTRACT

Pathogenic bacteria encounter various stressors while residing in the host. They respond through intricate mechanisms of gene expression regulation, ensuring their survival and adaptation. Understanding how bacteria adapt to different stress conditions through regulatory processes of specific genes requires exploring complex transcriptional responses using gene co-expression networks. We employed a large transcriptome data set comprising 32 diverse human bacterial pathogens exposed to the same 11 host-mimicking stress conditions. Using the weighted gene co-expression network analysis algorithm, we generated bacterial gene co-expression networks. By associating modular eigengene expression with specific stress conditions, we identified gene co-expression modules and stress-specific stimulons, including genes with unique expression patterns under specific stress conditions. Suggesting a new potential role of the
frm
operon in responding to bile stress in enteropathogenic bacteria demonstrates the effectiveness of our approach. We also revealed the regulation of streptolysin S genes, involved in the production, processing, and export of streptolysin S, a toxin responsible for the β-hemolytic phenotype of group A
Streptococcus
. In a comparative analysis of stress responses in three
Escherichia coli
strains from the core transcriptome, we revealed shared and unique expression patterns across the strains, offering insights into convergent and divergent stress responses. To help researchers perform similar analyses, we created the user-friendly web application Co-PATHOgenex. This tool aids in deepening our understanding of bacterial adaptation to stress conditions and in deciphering complex transcriptional responses of bacterial pathogens.

IMPORTANCE

Unveiling gene co-expression networks in bacterial pathogens has the potential for gaining insights into their adaptive strategies within the host environment. Here, we developed Co-PATHOgenex, an interactive and user-friendly web application that enables users to construct networks from gene co-expressions using custom-defined thresholds (
https://avicanlab.shinyapps.io/copathogenex/)
. The incorporated search functions and visualizations within the tool simplify the usage and facilitate the interpretation of the analysis output. Co-PATHOgenex also includes stress stimulons for various bacterial species, which can help identify gene products not previously associated with a particular stress condition.
High-performance enrichment-based genome sequencing to support the investigation of hepatitis A virus outbreaks
Authors: Zufan Sara E. , Mercoulia Karolina , Kwong Jason C. , Judd Louise M. , Howden Benjamin P. , Seemann Torsten , Stinear Timothy P. 
Published: November 2023

ABSTRACT
Hepatitis A virus (HAV) infections are an increasing public health concern in low-endemicity regions due to outbreaks from food-borne infections and sustained transmission among vulnerable groups, including persons experiencing homelessness, those who inject drugs, and men who have sex with men, which is further compounded by aging, unvaccinated populations. DNA sequence characterization of HAV for source tracking is performed by comparing small subgenomic regions of the virus. While this approach has been successful when robust epidemiological data are available, poor genetic resolution can lead to the conflation of outbreaks with sporadic cases. HAV outbreak investigations would greatly benefit from the additional phylogenetic resolution obtained by whole virus genome sequence comparisons. However, HAV genomic approaches can be difficult because of challenges in isolating the virus, low sensitivity of direct metagenomic sequencing in complex sample matrices like various foods, such as fruits, vegetables, and molluscs, and difficulty designing highly multiplexed PCR primers across diverse HAV genotypes. Here, we introduce a proof-of-concept pan-HAV oligonucleotide hybrid capture enrichment assay from serum and frozen berry specimens that yields complete and near-complete HAV genomes from as few as four input HAV genome copies. We used this method to recover HAV genomes from human serum specimens with high Cτ values (34.7–42.7), with high assay performance for all six human HAV subgenotypes, both contemporary and historical. Our approach provides a highly sensitive and streamlined workflow for HAV whole-genome sequencing from diverse sample types that can be the basis for harmonized and high-resolution molecular epidemiology during HAV outbreak surveillance.

IMPORTANCE
This proof-of-concept study introduces a hybrid capture oligo panel for whole-genome sequencing of all six human pathogenic hepatitis A virus (HAV) subgenotypes, exhibiting a higher sensitivity than some conventional genotyping assays. The ability of hybrid capture to enrich multiple targets allows for a single, streamlined workflow, thus facilitating the potential harmonization of molecular surveillance of HAV with other enteric viruses. Even challenging sample matrices can be accommodated, making them suitable for broad implementation in clinical and public health laboratories. This innovative approach has significant implications for enhancing multijurisdictional outbreak investigations as well as our understanding of the global diversity and transmission dynamics of HAV.
Transcriptome profiling of type VI secretion system core gene
tssM
mutant of
Xanthomonas perforans
highlights regulators controlling diverse functions ranging from virulence to metabolism
Authors: Ramamoorthy Sivakumar , Pena Michelle , Ghosh Palash , Liao Ying-Yu , Paret Mathews , Jones Jeffrey B. , Potnis Neha 
Published: November 2023

ABSTRACT

Type VI secretion system (T6SS) is a versatile, contact-dependent contractile nano-weapon in Gram-negative bacteria that fires proteinaceous effector molecules directly into prokaryotic and eukaryotic cells aiding in manipulation of the host and killing of competitors in complex niches. In plant pathogenic xanthomonads, T6SS has been demonstrated to play these diverse roles in individual pathosystems. However, the molecular network underlying the regulation of T6SS is still elusive in
Xanthomonas
spp. To bridge this knowledge gap, we conducted an
in vitro
transcriptome screen using plant apoplast mimicking minimal medium, XVM2 medium, to decipher the effect of
tssM
deletion, a core gene belonging to T6SS-cluster i3*, on the regulation of gene expression in
Xanthomonas perforans
strain AL65. Transcriptomic data revealed that a total of 277 and 525 genes were upregulated, while 307 and 392 genes were downregulated in the mutant strain after 8 and 16 hours of growth in XVM2 medium. The transcript abundance of several genes associated with flagellum and pilus biogenesis as well as type III secretion system was downregulated in the mutant strain. Deletion of
tssM
of cluster-i3* resulted in upregulation of several T6SS genes belonging to cluster-i3*** and genes involved in biofilm and cell wall biogenesis. Similarly, transcription regulators like
rpoN
, Pho regulon,
rpoE
, and
csrA
were identified to be upregulated in the mutant strain. Our results suggest that T6SS modulates the expression of global regulators like
csrA
,
rpoN
, and
pho
regulons, triggering a signaling cascade, and co-ordinates the expression of suite of virulence factors, stress response genes, and metabolic genes.

IMPORTANCE

T6SS has received attention due to its significance in mediating interorganismal competition through contact-dependent release of effector molecules into prokaryotic and eukaryotic cells. Reverse-genetic studies have indicated the role of T6SS in virulence in a variety of plant pathogenic bacteria, including the one studied here,
Xanthomonas
. However, it is not clear whether such effect on virulence is merely due to a shift in the microbiome-mediated protection or if T6SS is involved in a complex virulence regulatory network. In this study, we conducted in vitro transcriptome profiling in minimal medium to decipher the signaling pathways regulated by tssM-i3* in
X. perforans
AL65. We show that TssM-i3* regulates the expression of a suite of genes associated with virulence and metabolism either directly or indirectly by altering the transcription of several regulators. These findings further expand our knowledge on the intricate molecular circuits regulated by T6SS in phytopathogenic bacteria.
miR-26a exerts broad-spectrum antiviral effects via the enhancement of RIG-I-mediated type I interferon response by targeting USP15
Authors: Zhang Jikai , Li Chunyang , Hou Yao , Liu Dan , Li Qiudi , Wang Zijie , Tang Renxian , Zheng Kuiyang , Guo Hongbo , Wang Wenshi 
Published: November 2023

ABSTRACT
Host innate immunity is an important defense line against virus infection and is precisely regulated by various factors. Studying the mechanism of virus-host interaction is essential to developing novel antivirals. Being one of the key host natural antiviral responses, host small non-coding RNAs (miRNAs) possess promising antiviral potential worthy of study. Herein, we found that miR-26a exerted broad-spectrum antiviral effect against multiple viruses, e.g., Hepatitis E virus, Vesicular Stomatitis Virus, and Sendai Virus. Mechanistically, miR-26a specifically targets 3′UTR of mRNA to inhibit USP15 expression. USP15 interacted directly with RIG-I to deubiquitinate K63-linked RIG-I, thus negatively regulating type I interferon (IFN) signaling. Consequently, miR-26a, by downregulating USP15, promotes K63 ubiquitination of RIG-I to enhance type I IFN responses, resulting in an active antiviral state against virus infection. Intriguingly, the activation of type I IFN responses could suppress miR-26a expression, serving as an intrinsic negative feedback loop to avoid dysregulated signal activation. Hence, the broad-spectrum antiviral effects of miR-26a and its mode-of-action enriched the interaction networks between miRNAs and innate immunity, providing insights for the development of broad-spectrum antivirals against viral infection.

IMPORTANCE
miR-26a serves as a potent positive regulator of type I interferon (IFN) responses. By inhibiting USP15 expression, miR-26a promotes RIG-I K63-ubiquitination to enhance type I IFN responses, resulting in an active antiviral state against viruses. Being an intricate regulatory network, the activation of type I IFN responses could in turn suppress miR-26a expression to avoid the disordered activation that might result in the so-called “type I interferonopathy.” The knowledge gained would be essential for the development of novel antiviral strategies against viral infection.
Loss of
Bacteroides thetaiotaomicron
bile acid-altering enzymes impacts bacterial fitness and the global metabolic transcriptome
Authors: McMillan Arthur S. , Foley Matthew H. , Perkins Caroline E. , Theriot Casey M. 
Published: November 2023

ABSTRACT

Bacteroides thetaiotaomicron
(
B. theta
) is a Gram-negative gut bacterium that encodes enzymes that alter the bile acid pool in the gut. Primary bile acids are synthesized by the host liver and are modified by gut bacteria.
B. theta
encodes two bile salt hydrolases, as well as a hydroxysteroid dehydrogenase. We hypothesize that
B. theta
modifies the bile acid pool in the gut to provide a fitness advantage for itself. To investigate each gene’s role, different combinations of genes encoding bile acid-altering enzymes (
bshA
,
bshB
, and
hsdhA
) were knocked out by allelic exchange, including a triple KO. Bacterial growth and membrane integrity assays were done in the presence and absence of bile acids. To explore if
B. theta’s
response to nutrient limitation changes due to the presence of bile acid-altering enzymes, RNA sequencing (RNASeq) analysis of wild type (WT) and triple knockout (KO) strains in the presence and absence of bile acids was done. WT
B. theta
is more sensitive to deconjugated bile acids such as cholate, chenodeoxycholate (CDCA), and deoxycholate (DCA) compared with the triple KO. These deconjugated bile acids also decreased membrane integrity of both WT and triple KO. The presence of
bshB
is detrimental to growth in conjugated forms of CDCA and DCA. RNASeq analysis also showed that bile acid exposure impacts multiple metabolic pathways in
B. theta
, but DCA significantly increases expression of many genes in carbohydrate metabolism, specifically those in polysaccharide utilization loci or PULs, in nutrient-limited conditions. This study suggests that bile acids
B. theta
encounters in the gut may signal the bacterium to increase or decrease its utilization of carbohydrates. Further study looking at the interactions between bacteria, bile acids, and the host may inform rationally designed probiotics and diets to ameliorate inflammation and disease.

IMPORTANCE

Recent work on bile salt hydrolases (BSHs) in Gram-negative bacteria, such as Bacteroides, has primarily focused on how they can impact host physiology. However, the benefits bile acid metabolism confers to the bacterium that performs it are not well understood. In this study, we set out to define if and how
Bacteroides thetaiotaomicron
(
B. theta
) uses its BSHs and hydroxysteroid dehydrogenase to modify bile acids to provide a fitness advantage for itself
in vitro
and
in vivo
. Genes encoding bile acid-altering enzymes were able to impact how
B. theta
responds to nutrient limitation in the presence of bile acids, specifically carbohydrate metabolism, affecting many polysaccharide utilization loci. This suggests that
B. theta
may be able to shift its metabolism, specifically its ability to target different complex glycans including host mucin, when it comes into contact with specific bile acids in the gut.
Einstein Manifold of SO(p, 9 – p), Its Corresponding Parabolic Subgroup, and Invariant Differential Operators
Authors: Dobrev V. K. 
Published: November 2023

AbstractIn the present paper we continue the project of systematic explicit construction of invariant differential operators. On the example of the non-compact group$$SO(p,9 - p)$$(for$$p = 5,6$$) we give the classification multiplets of indecomposable elementary representations induced from suitable choice of parabolic subgroup$$MAN$$so that the factor-group$${G \mathord{\left/ {\vphantom {G M}} \right. \kern-0em} M}$$is an Einstein manifold. This classification includes the data for the relevant invariant differential operators.
A youth-centred approach to improving engagement in HIV services: human-centred design methods and outcomes in a research trial in Kisumu County, Kenya
Authors: Akama Eliud Omondi , Beres Laura K , Kulzer Jayne Lewis , Ontuga Gladys , Adhiambo Harriet , Bushuru Sarah , Nyagesoa Edwin , Osoro Joseph , Opondo Isaya , Sang Norton , Oketch Bertha , Nyanga James , Osongo Cirilus Ogollah , Nyandieka Evelyn , Ododa Evelyn , Omondi Eunice , Ochieng Felix , Owino Clinton , Odeny Thomas , Kwena Zachary Arochi , Eshun-Wilson Ingrid , Petersen Maya , Bukusi Elizabeth A , Geng Elvin H , Abuogi Lisa L 
Published: November 2023

IntroductionInnovative interventions are needed to improve HIV outcomes among adolescents and young adults (AYAs) living with HIV. Engaging AYAs in intervention development could increase effectiveness and youth acceptance, yet research is limited. We applied human-centred design (HCD) to refine adherence-support interventions pretrial and assessed HCD workshop acceptability.MethodsWe applied an iterative, four-phased HCD process in Kenya that included: (1) systematic review of extant knowledge, (2) prioritisation of design challenges, (3) a co-creation workshop and (4) translation tables to pair insights with trial intervention adaptations. The co-creation workshop was co-led by youth facilitators employing participatory activities to inform intervention adaptations. Iterative data analysis included rapid thematic analysis of visualised workshop outputs and notes using affinity mapping and dialogue to identify key themes. We conducted a survey to assess workshop acceptability among participants.ResultsTwenty-two participants engaged in the 4-day workshop. Co-creation activities yielded recommendations for improving planned interventions (eg, message frequency and content; strategies to engage hard-to-reach participants), critical principles to employ across interventions (eg, personalisation, AYA empowerment) and identification of unanticipated AYA HIV treatment priorities (eg, drug holidays, transition from adolescent to adult services). We revised intervention content, peer navigator training materials and study inclusion criteria in response to findings. The youth-led HCD workshop was highly acceptable to participants.ConclusionsResearch employing HCD among youth can improve interventions preimplementation through empathy, youth-led inquiry and real-time problem solving. Peer navigation may be most influential in improving retention when engagement with young people is based on mutual trust, respect, privacy and extends beyond HIV-specific support. Identifying opportunities for personalisation and adaptation within intervention delivery is important for AYAs. Patient engagement interventions that target young people should prioritise improved transition between youth and adult services, youth HIV status disclosure, AYA empowerment and healthcare worker responsiveness in interactions and episodic adherence interruptions.