Identification and specificity validation of unique and antimicrobial resistance genes to trace suspected pathogenic AMR bacteria and to monitor the development of AMR in non-AMR strains in the environment and clinical settings
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ABSTRACT:
SUBMITTER: Rekadwad B
PROVIDER: S-EPMC10696110 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:Recent studies have focused on the identification and manipulation of memory traces in rodent models. The two main mouse models utilized are either a CreER(T2) /loxP tamoxifen (TAM)- or a tetracycline transactivator/tetracycline-response element doxycycline-inducible system. These systems, however, could be improved to label a more specific population of activated neurons corresponding to behavior. Here, we sought to identify an improved selective estrogen receptor (ER) modulator (SERM) in which we could label an individual memory trace in ArcCreER(T2) mice. We found that 4-hydroxytamoxifen (4-OHT) is a selective SERM in the ArcCreER(T2) × Rosa26-CAG-stop(flox) -channelrhodospin (ChR2)-enhanced yellow fluorescent protein (eYFP) mice. The half-life of 4-OHT is shorter than TAM, allowing for more specificity of memory trace labeling. Furthermore, 4-OHT allowed for context-specific labeling in the dentate gyrus and CA3. In summary, we believe that 4-OHT improves the specificity of memory trace labeling and will allow for refined memory trace studies in the future. © 2015 Wiley Periodicals, Inc.
| S-EPMC4867142 | biostudies-literature
Project description:Mucormycosis is an increasingly common, life-threatening fungal infection caused by fungi belonging to the subphylum Mucormycotina, order Mucorales. The major risk factors for mucormycosis include uncontrolled diabetes mellitus, treatment with corticosteroids, organ or bone marrow transplantation, neutropenia, trauma and burns, malignant hematological disorders, and deferoxamine-therapy in patients receiving hemodialysis. Amphotericin B (AmB) remains the only antifungal agent approved for the treatment of invasive mucormycosis. Because fungi belonging to the mucorales order are relatively resistant to AmB, high doses are required, which frequently causes nephrotoxicity and other adverse effects. In the absence of surgical removal of the infected focus (such as excision of the eye in patients with rhinocerebral mucormycosis), antifungal therapy alone is rarely curative. Even when surgical debridement is combined with high-dose AmB, the mortality associated with mucor¬mycosis is >50%. In patients with prolonged neutropenia or disseminated disease, mortality is 90-100%. Rhizopus oryzae is by far the most common organism isolated from patients with mucormycosis, and is responsible for approximately 70% of all cases of mucormycosis. Recent epidemiological data collected from transplant centers have demonstrated a striking increase in the number of reported cases of mucormycosis. Furthermore, mucormycosis outbreaks are also known to follow natural disasters as was the case following the tsunami that devastated Indonesia in 2004 and the tornadoes that destroyed Joplin, Missouri in June 2011. Hence, there exists a large impetus to identify particular virulence factors and biomarkers associated with mucormycosis, which would lead to a rational approach to develop new antifungals and vaccines to prevent deaths specifically due to mucormycosis. In order to better understand the complex nature of the host pathogen interaction during mucormycosis, we performed dual species RNA-seq on 5 different Mucorales strains during in vitro infection of endothelial or epithelial cells.
2014-06-19 | GSE58634 | GEO
Project description:Although research has increasingly focused on the pathogenesis of avian pathogenic Escherichia coli (APEC) infections and the "APEC pathotype" itself, little is known about the reservoirs of these bacteria. We therefore compared outbreak strains isolated from diseased chickens (n = 121) with nonoutbreak strains, including fecal E. coli strains from clinically healthy chickens (n = 211) and strains from their environment (n = 35) by determining their virulence gene profiles, phylogenetic backgrounds, responses to chicken serum, and in vivo pathogenicities in a chicken infection model. In general, by examining 46 different virulence-associated genes we were able to distinguish the three groups of avian strains, but some specific fecal and environmental isolates had a virulence gene profile that was indistinguishable from that determined for outbreak strains. In addition, a substantial number of phylogenetic EcoR group B2 strains, which are known to include potent human and animal extraintestinal pathogenic E. coli (ExPEC) strains, were identified among the APEC strains (44.5%) as well as among the fecal E. coli strains from clinically healthy chickens (23.2%). Comparably high percentages (79.2 to 89.3%) of serum-resistant strains were identified for all three groups of strains tested, bringing into question the usefulness of this phenotype as a principal marker for extraintestinal virulence. Intratracheal infection of 5-week-old chickens corroborated the pathogenicity of a number of nonoutbreak strains. Multilocus sequence typing data revealed that most strains that were virulent in chicken infection experiments belonged to sequence types that are almost exclusively associated with extraintestinal diseases not only in birds but also in humans, like septicemia, urinary tract infection, and newborn meningitis, supporting the hypothesis that not the ecohabitat but the phylogeny of E. coli strains determines virulence. These data provide strong evidence for an avian intestinal reservoir hypothesis which could be used to develop intestinal intervention strategies. These strains pose a zoonotic risk because either they could be transferred directly from birds to humans or they could serve as a genetic pool for ExPEC strains.
| S-EPMC2612213 | biostudies-literature
Project description:BackgroundEnsuring accurate and continuous monitoring of patients' physiological parameters is paramount for evaluating their health status and guiding clinical decision-making. Technological advancements have the potential to significantly improve patient care and outcomes by offering a seamless continuum of healthcare experiences. Biobeat Technologies Ltd has pioneered a non-invasive wearable approach to acquiring advanced hemodynamic parameters, employing devices such as the BB-613WP wrist monitor and the BB-613P chest patch. Biobeat devices have been applicable across many clinical settings, as substantiated by a growing body of research. This systematic review endeavours to comprehensively consolidate the evidence regarding using Biobeat monitors across various clinical scenarios.MethodsFrom 2016 to 2024, a thorough literature search was conducted across multiple databases. The inclusion criteria for selected studies comprised adult patients aged 18 years or older in any healthcare setting, employing Biobeat monitoring devices (wrist monitors and/or chest patches), reporting at least one outcome or finding, and presenting fully published original research studies, including randomized controlled trials and prospective or retrospective cohort studies. The quality and risk of bias assessment for the studies was performed using the Newcastle-Ottawa scale and COSMIN scoring system.ResultsAmong 27 studies identified, 15 met the inclusion criteria, involving 4248 patients. These included 14 prospective observational studies and one retrospective cohort study; no randomized control trials were identified. Notably, eight studies were conducted in ambulatory settings, with 1 study focusing on patients undergoing labor and delivery. Additionally, three studies were carried out in general inpatient wards, 1 in a medical ICU and another in a cardiac surgery ICU (CSICU). Furthermore, 1 study presented results from 3 separate investigations- 2 in ambulatory settings and 1 in the CSICU. Across all studies, Biobeat devices were consistently utilized, with each study reporting positive outcomes associated with their use.ConclusionThis systematic review demonstrates that Biobeat's non-invasive wearable devices have been effectively utilized across various clinical settings, consistently contributing to positive patient outcomes. The versatility and reliability of these devices highlight their potential to enhance patient care and support clinical decision-making, warranting further research to explore their broader applications.
| S-EPMC11866379 | biostudies-literature
Project description:Unique marine environment-1 Raw sequence reads
| PRJNA817068 | ENA
Project description:Comparative ‘omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli
| PRJEB23469 | ENA
Project description:Thraustochytrids are heterotrophic marine protists that are considered as important decomposers in the marine ecosystem; however, how they digest and uptake lipid nutrients from the environment is largely unknown. Genomic clustering analysis using thraustochytrid draft genome databases revealed that novel proteins with a Lipase_3 domain are commonly present in thraustochytrids, including Aurantiochytrium limacinum. After heterologous expression and His tag-based purification, protein ID: 145138 was identified as lipase/phospholipase capable of hydrolyzing triacylglycerol (TG) and phosphatidylcholine (PC). 145138 was secreted into the medium, and deletion of the 145138 gene in A. limacinum reduced the degradation of extracellular lipids. Fatty acids generated by 145138 were reused for the biosynthesis of PC and TG, and 145138 allowed A. limacinum to survive in the medium containing TG as a sole carbon source. 145138 hydrolyzed all the acyl-ester linkages of TG; however, the enzyme showed strict positional specificity toward phospholipids, generating 2-acyl lysophospholipids. The 2-acyl lysophospholipids showed stronger antimicrobial activity compared with 1-acyl lysophospholipids. These results suggested that 145138 is a bifunctional enzyme that contributes to the acquisition of lipid nutrients from the environment, as well as to generate antimicrobial lysophospholipids that are beneficial for competition with bacteria over lipid nutrients in the marine environment.
| S-EPMC6841712 | biostudies-literature
Project description:IntroductionIn recent years much progress has been made in the development of tools for systems biology to study the levels of mRNA and protein, and their interactions within cells. However, few multiplexed methodologies are available to study cell signalling directly at the transcription factor level.MethodsHere we describe a sensitive, plasmid-based RNA reporter methodology to study transcription factor activation in mammalian cells, and apply this technology to profiling 60 transcription factors in parallel. The methodology uses two robust and easily accessible detection platforms; quantitative real-time PCR for quantitative analysis and DNA microarrays for parallel, higher throughput analysis.FindingsWe test the specificity of the detection platforms with ten inducers and independently validate the transcription factor activation.ConclusionsWe report a methodology for the multiplexed study of transcription factor activation in mammalian cells that is direct and not theoretically limited by the number of available reporters.
| S-EPMC3510088 | biostudies-literature
Project description:Avian pathogenic Escherichia coli (APEC) is an important bacterial pathogen that causes avian colibacillosis and leads to huge economic losses in the poultry industry. Different virulence traits contribute to pathogenesis of APEC infections, and antimicrobial resistance (AMR) has also been an overwhelming issue in poultry worldwide. In the present study, we aimed to investigate and compare the presence of virulence-associated genes (VAGs), AMR, and phylogenetic group's distribution among APEC and avian fecal E. coli (AFEC) strains. E. coli from birds with colisepticemia and yolk sac infection (YSI) (APEC) plus E. coli strains from the feces of healthy birds (AFEC) were compared by the aforementioned traits. In addition, the clonal relatedness was compared using Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). Although all strains were susceptible to fosfomycin, ceftriaxone, and cefixime, almost all strains (98%) were multi-drug resistant (MDR). All strains (except two) harbored at least three or more VAGs, and the virulence scores tended to be higher in pathogenic strains especially in the colisepticemic group. All phylogenetic groups were found in isolates from YSI, colisepticemia, and the feces of healthy birds; however, the frequency of phylogroups varied according to the source of the isolate. B1 and C phylogroups were statistically more likely to be found among APEC from YSI and colisepticemic E. coli groups, respectively, while phylogroup A was the most frequently occurring phylogroup among AFEC strains. Our findings also revealed that AMR and VAGs are not essentially co-evolved traits as in some instances AMR strains were more prevalent among AFEC. This reflects the divergent evolutionary pathways of resistance acquisition in pathogenic or non-pathogenic avian E. coli strains. Importantly, strains related to phylogenetic group C showed higher virulence score and AMR that requires further attention. To some extent, ERIC-PCR was able to group strains by isolation source, phylogroup, or virulence genes. Further integrated studies along with assessment of more detailed genotypic and phenotypic features could potentially lead to better understanding of virulence, resistance, and evolution of ExPEC.
| S-EPMC8651559 | biostudies-literature
Project description:Streptococcus suis type 2 strains that are pathogenic for pigs produce a 110-kDa extracellular protein factor (EF). Nonpathogenic and weakly pathogenic strains do not produce EF or produce a protein (EF*) that is immunologically related to EF. To study the pathogenesis of S. suis type 2 in pigs and to develop tools and methods for the control of S. suis type 2 infections, we cloned and characterized the genes encoding EF and various EF* proteins. Analysis of the deduced amino acid sequences showed that the first 833 amino acids at the N terminus of the EF and EF* proteins were nearly identical. The proteins differed, however, at their C termini. Unlike the 110-kDa EF protein, the EF* proteins contained several repeated units of 76 amino acids. The number and arrangement of the repeats in the EF* proteins varied. The data suggest that the gene encoding EF could have evolved from an epf* gene by a specific deletion event. The lack of repeated amino acid units in the EF protein may be related to virulence.
| S-EPMC281006 | biostudies-other