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Microbiology Spectrum Jul 2024Rapid detection of carbapenemase-producing Enterobacteriaceae (CPE) is urgently needed to prevent their spread in healthcare settings. Here, we have evaluated the... (Comparative Study)
Comparative Study
Rapid detection of carbapenemase-producing Enterobacteriaceae (CPE) is urgently needed to prevent their spread in healthcare settings. Here, we have evaluated the performance of the phenotypic methods for detection of carbapenemase production directly from bacterial cultures. A total of 99 clinical and rectal Enterobacteriaceae isolates were included (81 carrying known carbapenemase-encoding genes and 18 without carbapenemase production). All isolates were subjected to the five phenotypic tests including in-house Carba NP (iCarba NP), modified-Carba NP, E-Test MBL, modified Hodge test (MHT), and commercial combination disk test. Test results were read at different time points for iCarba NP and modified-Carba (1 min, 5 min, 15 min, 1 h and 2 h). The sensitivity and specificity of the iCarba NP were 78.87% and 100%, respectively, whereas those of the modified-Carba NP test were 95.06% and 94.44%, respectively. False-negative results were detected in four OXA-48 isolates with the use of modified-Carba NP, whereas one non-carbapenemase isolate had false-positive results. The sensitivity/specificity was 91.30%/100% and 80.25%/83.33% for the E-Test MBL and MHT, respectively. The sensitivity and specificity of the aminophenylboronic acid synergy test were 100% and 97.94%, respectively, whereas those of the dipicolinic acid synergy test were 82.61% and 96.23%, respectively. Rapid, simple, and reliable methods are needed for laboratory detection of CPE isolates to improve the detection and surveillance of these clinically relevant pathogens in an epidemiological context. We conclude that the modified-Carba NP test can be one of the reliable tests for the prediction of carbapenemase-producing bacteria.IMPORTANCEThe emergence of carbapenem resistance among Gram-negative bacteria is a serious global health threat. Here, we investigate the performance of the five phenotypic assays against carbapenemase-producing and carbapenemase-non-producing Enterobacteriaceae. Accurate and rapid detection of CPE isolates is critically required for clinical management and treatment of infections caused by these organisms. Among the five evaluated phenotypic tests, the mCNP test presented the highest sensitivity (95.06%) and, therefore, can be considered the best test to be used as a screening phenotypic methodology.
Topics: Bacterial Proteins; beta-Lactamases; Humans; Enterobacteriaceae Infections; Carbapenem-Resistant Enterobacteriaceae; Sensitivity and Specificity; Microbial Sensitivity Tests; Phenotype; Anti-Bacterial Agents; Enterobacteriaceae
PubMed: 38832776
DOI: 10.1128/spectrum.00386-24 -
Microbiology Spectrum Jul 2024Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen . Unfortunately, patients are often misdiagnosed with bacterial pneumonia,...
UNLABELLED
Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen . Unfortunately, patients are often misdiagnosed with bacterial pneumonia, leading to inappropriate antibiotic treatment. The soil -like species exhibits antagonistic properties against ; however, the antagonistic capabilities of host microbiota against are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of . We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of while partial depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2×GYE (GYE) and Columbia colistin and nalidixic acid with 5% sheep's blood agar inhibited the growth of , but microbiota grown on chocolate agar did not. Partial depletion of the microbiota through antibiotic disk diffusion revealed diminished inhibition and comparable growth of to controls. To characterize the bacteria grown and identify potential candidates contributing to the inhibition of , 16S rRNA sequencing was performed on tracheal and intestinal agar cultures and murine lung extracts. We found that the host bacteria likely responsible for this inhibition primarily included and . The results of this study demonstrate the potential of the host microbiota to inhibit the growth of and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth .
IMPORTANCE
Coccidioidomycosis is caused by a fungal pathogen that invades the host lungs, causing respiratory distress. In 2019, 20,003 cases of Valley fever were reported to the CDC. However, this number likely vastly underrepresents the true number of Valley fever cases, as many go undetected due to poor testing strategies and a lack of diagnostic models. Valley fever is also often misdiagnosed as bacterial pneumonia, resulting in 60%-80% of patients being treated with antibiotics prior to an accurate diagnosis. Misdiagnosis contributes to a growing problem of antibiotic resistance and antibiotic-induced microbiome dysbiosis; the implications for disease outcomes are currently unknown. About 5%-10% of symptomatic Valley fever patients develop chronic pulmonary disease. Valley fever causes a significant financial burden and a reduced quality of life. Little is known regarding what factors contribute to the development of chronic infections and treatments for the disease are limited.
Topics: Animals; Coccidioides; Mice; Gastrointestinal Microbiome; Trachea; Coccidioidomycosis; Microbiota; Bacteria; Female; Anti-Bacterial Agents; RNA, Ribosomal, 16S
PubMed: 38832766
DOI: 10.1128/spectrum.02978-23 -
PloS One 2024Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins....
Extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) is an emerging pathogen of high concern given its resistance to extended-spectrum cephalosporins. Broiler chicken, which is the number one consumed meat in the United States and worldwide, can be a reservoir of ESBL E. coli. Backyard poultry ownership is on the rise in the United States, yet there is little research investigating prevalence of ESBL E. coli in this setting. This study aims to identify the prevalence and antimicrobial resistance profiles (phenotypically and genotypically) of ESBL E. coli in some backyard and commercial broiler farms in the U.S. For this study ten backyard and ten commercial farms were visited at three time-points across flock production. Fecal (n = 10), litter/compost (n = 5), soil (n = 5), and swabs of feeders and waterers (n = 6) were collected at each visit and processed for E. coli. Assessment of ESBL phenotype was determined through using disk diffusion with 3rd generation cephalosporins, cefotaxime and ceftazidime, and that with clavulanic acid. Broth microdilution and whole genome sequencing were used to investigate both phenotypic and genotypic resistance profiles, respectively. ESBL E. coli was more prevalent in backyard farms with 12.95% of samples testing positive whereas 0.77% of commercial farm samples were positive. All isolates contained a blaCTX-M gene, the dominant variant being blaCTX-M-1, and its presence was entirely due to plasmids. Our study confirms concerns of growing resistance to fourth generation cephalosporin, cefepime, as roughly half (51.4%) of all isolates were found to be susceptible dose-dependent and few were resistant. Resistance to non-beta lactams, gentamicin and ciprofloxacin, was also detected in our samples. Our study identifies prevalence of blaCTX-M type ESBL E. coli in U.S. backyard broiler farms, emphasizing the need for interventions for food and production safety.
Topics: Animals; beta-Lactamases; Escherichia coli; Chickens; United States; Plasmids; Escherichia coli Infections; Prevalence; Anti-Bacterial Agents; Poultry Diseases; Microbial Sensitivity Tests; Feces; Escherichia coli Proteins; Farms
PubMed: 38829840
DOI: 10.1371/journal.pone.0304599 -
Translational Vision Science &... Jun 2024Deep learning architectures can automatically learn complex features and patterns associated with glaucomatous optic neuropathy (GON). However, developing robust...
PURPOSE
Deep learning architectures can automatically learn complex features and patterns associated with glaucomatous optic neuropathy (GON). However, developing robust algorithms requires a large number of data sets. We sought to train an adversarial model for generating high-quality optic disc images from a large, diverse data set and then assessed the performance of models on generated synthetic images for detecting GON.
METHODS
A total of 17,060 (6874 glaucomatous and 10,186 healthy) fundus images were used to train deep convolutional generative adversarial networks (DCGANs) for synthesizing disc images for both classes. We then trained two models to detect GON, one solely on these synthetic images and another on a mixed data set (synthetic and real clinical images). Both the models were externally validated on a data set not used for training. The multiple classification metrics were evaluated with 95% confidence intervals. Models' decision-making processes were assessed using gradient-weighted class activation mapping (Grad-CAM) techniques.
RESULTS
Following receiver operating characteristic curve analysis, an optimal cup-to-disc ratio threshold for detecting GON from the training data was found to be 0.619. DCGANs generated high-quality synthetic disc images for healthy and glaucomatous eyes. When trained on a mixed data set, the model's area under the receiver operating characteristic curve attained 99.85% on internal validation and 86.45% on external validation. Grad-CAM saliency maps were primarily centered on the optic nerve head, indicating a more precise and clinically relevant attention area of the fundus image.
CONCLUSIONS
Although our model performed well on synthetic data, training on a mixed data set demonstrated better performance and generalization. Integrating synthetic and real clinical images can optimize the performance of a deep learning model in glaucoma detection.
TRANSLATIONAL RELEVANCE
Optimizing deep learning models for glaucoma detection through integrating DCGAN-generated synthetic and real-world clinical data can be improved and generalized in clinical practice.
Topics: Deep Learning; Humans; Optic Disk; Optic Nerve Diseases; ROC Curve; Glaucoma; Female; Male; Middle Aged; Algorithms
PubMed: 38829624
DOI: 10.1167/tvst.13.6.1 -
Frontiers in Veterinary Science 2024Two medium-sized, 7-year-old dogs, with no previous history of pain, presented with acute neurologic symptoms consistent with intervertebral disk disease. Both cases had...
Two medium-sized, 7-year-old dogs, with no previous history of pain, presented with acute neurologic symptoms consistent with intervertebral disk disease. Both cases had CT, where cervical pathology was identified. In one dog, the diagnosis was singular extensive cervical disk herniation with possible epidural hemorrhage and in the other, the diagnosis was multiple-site cervical disk herniation. The first dog, a Shar-Pei, underwent treatment with two standard adjacent ventral slots between the C4-C5 and C5-C6 intervertebral disk spaces and a fenestration between the C3 and C4 intervertebral disk spaces. The second case, a beagle, underwent a double adjacent standard ventral slot between the C5-C6 and C6-C7 intervertebral disk spaces. Both dogs recovered uneventfully after the surgery and showed no signs of recurrence during a 2-year follow-up period. This is the first detailed report of the use of a double adjacent ventral slot as a treatment for spinal decompression in medium-sized dogs with multiple-site spinal cord compression.
PubMed: 38828368
DOI: 10.3389/fvets.2024.1346816 -
Archives of Razi Institute Dec 2023Bacteriocins are a kind of antimicrobial peptides that kill or inhibit the growth of bacterial strains. The purpose of this study was to investigate the antibacterial...
Bacteriocins are a kind of antimicrobial peptides that kill or inhibit the growth of bacterial strains. The purpose of this study was to investigate the antibacterial effect of on several pathogenic bacterial strains. Bacteriocin produced by was purified by chromatography with Sephadex G-75 column, and its antibacterial effect on gram-negative bacteria, including ATCC 700928, PTCC 1707, PTCC 1621, PTCC 1693, and PTCC 1755, were evaluated by the disk diffusion method. The structure of bacteriocin was determined by nuclear magnetic resonance spectroscopy. The interaction of bacteriocin with the antigen 43 (Ag43) of was evaluated by the molecular docking method. Bacteriocin extracted from bacterial isolates had antibacterial activity on strains but not on other studied strains. Bioinformatics analysis also showed bacteriocin docking with Ag43 with an energy of -159.968 kJ/mol. Natural compounds, such as bacteriocin, can be an alternative to common chemical compounds and antibiotics. To reach a definite conclusion in this regard, there is a need for further research and understanding of their mechanism of action.
Topics: Serratia marcescens; Anti-Bacterial Agents; Bacteriocins; Escherichia coli; Molecular Docking Simulation
PubMed: 38828162
DOI: 10.32592/ARI.2023.78.6.2694 -
Journal of Medical Physics 2024To explore the influence of initial guess or estimate (uniform as "ones" and "zeros" vs. filtered back projection [FBP] image) as an input image for maximum likelihood...
PURPOSE
To explore the influence of initial guess or estimate (uniform as "ones" and "zeros" vs. filtered back projection [FBP] image) as an input image for maximum likelihood expectation-maximization (MLEM) tomographic reconstruction algorithm and provide the curves of error or convergence for each of these three initial estimates.
METHODS
Two phantoms, created as digital images, were utilized: one was a simple noiseless object and the other was a more complicated, noise-degraded object of the section of lower thorax in a matrix of 256 × 256 pixels. Both underwent radon transform or forward projection process and the corresponding sinograms were generated. For filtering during tomographic image reconstruction, ramp and Butterworth filters, as high-pass and low-pass ones, were applied to images. The second phantom (lower thorax) was radon-transformed and the resulting sinogram was degraded by noise. As initial guess or estimate images, in addition to FBP tomographic image, two uniform images, one with all pixels having a value of 1 ("ones") and the other with all having zero ("zeros"), were created. The three initial estimates (FBP, ones, and zeros) were reconstructed with iterative MLEM tomographic reconstruction (with 1, 2, 4, 8, 16, 32, and 64 iterations). The difference between the object and the updated slice was calculated at the end of each iteration (as error matrix), and the mean squared error (MSE) was computed and plotted separately or in conjunction with the MSE curves of other initial estimates. All computations were implemented in MATLAB software.
RESULTS
The results of ones and zeros seemed strikingly similar. The curves of uniform ones and uniform zeros were so close to each other that overlap near-perfectly. However, in the FBP slice as an initial estimate, the resulting tomographic slice was similar with a much higher extent to the object even after 1 or 2 iterations. The pattern of convergence for all three curves was roughly similar. The normalized MSE decreased sharply up to 5 iterations and then, after 10 iterations, the curves reached a plateau until 32 iterations. For the phantom of the lower thorax section with its noise-degraded sinogram, similar to the pattern observed for simple disk-shaped phantom, the curves (normalized MSE) fell sharply up to 10 iterations and then rapidly converged thereafter until 64 iterations.
CONCLUSION
Similar results are observed when choosing different initial guesses or estimates (uniform vs. FBP) as the starting point, based on the error calculation using MSE. The algorithm converges almost similarly for all initial estimates. Therefore, selecting a uniform initial guess image can be an appropriate choice and may be preferred over an FBP image. Reducing the processing time can be a valid reason for this choice.
PubMed: 38828068
DOI: 10.4103/jmp.jmp_110_23 -
Frontiers in Neuroscience 2024Spinal cord injury is a condition affecting the central nervous system, causing different levels of dysfunction below the point of nerve damage. A 50-year-old woman...
Case report: Virtual reality-based arm and leg cycling combined with transcutaneous electrical spinal cord stimulation for early treatment of a cervical spinal cord injured patient.
Spinal cord injury is a condition affecting the central nervous system, causing different levels of dysfunction below the point of nerve damage. A 50-year-old woman suffered a neck injury as a result of a car accident. After undergoing posterior cervical C3-C6 internal fixation with titanium plates on one side and C7 lamina decompression, the patient, who had been diagnosed with C3-C7 cervical disk herniation and spinal stenosis causing persistent compression of the spinal cord, was transferred to the rehabilitation department. After implementing the combined therapy of Virtual Reality-based arm and leg cycling along with transcutaneous electrical stimulation of the spinal cord, the patients experienced a notable enhancement in both sensory and motor abilities as per the ASIA scores. The patient's anxiety and depression were reduced as measured by the Hamilton Anxiety and Hamilton Depression Tests. As evaluated by the SCIM-III, the patient's self-reliance and capacity to carry out everyday tasks showed ongoing enhancement, leading to the restoration of their functionality. Hence, the use of Virtual Reality-based arm and leg cycling along with transcutaneous electrical spinal cord stimulation has potential to positively impact function in patients with spinal cord injury. However, as this is a case report, the small number of patients and the fact that the intervention was initiated early after the injury, we were unable to separate the recovery due to the intervention from the natural recovery that is known to occur in the initial weeks and months after SCI. Therefore, further randomized controlled trials with a large sample size is necessary.
PubMed: 38826775
DOI: 10.3389/fnins.2024.1380467 -
Research Square May 2024one of the pathogens strongly implicated in hospital infections. Data on the resistance and molecular characteristics of this bacterium are rare in Mali.
BACKGROUND
one of the pathogens strongly implicated in hospital infections. Data on the resistance and molecular characteristics of this bacterium are rare in Mali.
OBJECTIVE
This study aimed to evaluate the antibiotic resistance patterns, virulence factors of isolates from pleural fluid infections in hospitalized patients.
METHODS
Pleural effusion samples were obtained by thoracentesis for bacteriological examination from October 2021 to December 2022 at the "Hôpital du Mali" teaching hospital. Comorbidities such as HIV/AIDS and diabetes were assessed. Standard microbiological procedures were used for bacterial identification. The disk diffusion method was used to identify methicillin-resistant . The PCR amplification method was used to detect the following genes: , , , , and .
RESULTS
This study analyzed 6096 samples from inpatients and found a pooled frequency of bacterial pleuritis of 526 (8.6%) in thoracic surgery and pediatric wards. was isolated in 52 (9.88%) cases, of which 39 (75%) isolates were MRSA. There was no significant difference between the sexes (). The median age of the patients was 30 years. All isolates showed resistance to penicillin-G. The leucocidin toxin was detected in 7.7% of thoracic surgery patients, but , , , and toxins were not found.
CONCLUSION
In this study, we found a high frequency of (and MRSA) in pleurisy patients at the "Hôpital du Mali". Only the leukocidin was found. The empirical treatment protocol for pleurisy may need revision. Clindamycin, linezolid, teicoplanin, daptomycin, fosfomycin, vancomycin, moxifloxacin and fusidic acid were the most active antibiotics on our isolates in this study. Infection prevention measures, active surveillance, and effective therapeutic options are recommended.
PubMed: 38826428
DOI: 10.21203/rs.3.rs-3579825/v1 -
Ecology and Evolution Jun 2024While morphological abnormalities have been widely reported in batomorphs, ontogenetic deformities of the posterior pectoral fin are rare. In this paper, we present two...
While morphological abnormalities have been widely reported in batomorphs, ontogenetic deformities of the posterior pectoral fin are rare. In this paper, we present two individuals of the bluespotted ribbontail ray, (Forsskål, 1775), with symmetrically deformed posterior pectoral fins. Both individuals were observed through aerial imagery on a coastal sandflat in the central Red Sea (22.30° N, 39.09° E). The similarity of this symmetrical deformity in both individuals indicates it likely has a genetic base. However, lacking access to the specimens, the ultimate cause of the abnormality remains uncertain. The incomplete disk closure did not seem to affect survival, as both individuals had reached a disk width of 22 cm, well above the typical birth size of the species. Our observations constitute both the first report of a morphological abnormality in and the first record of a batomorph with a symmetrically deformed posterior pectoral fin.
PubMed: 38826169
DOI: 10.1002/ece3.11399