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Frontiers in Public Health 2024nasal carriage has been linked to higher rates of infection and morbidity. People with Methicillin-resistant can be a potential source of infection for others....
Nasal carriage rate, associated factors, and antimicrobial susceptibility patterns of methicillin resistance among pre-clinical undergraduate students at the College of Health and Medical Sciences, Haramaya University, Ethiopia.
BACKGROUND
nasal carriage has been linked to higher rates of infection and morbidity. People with Methicillin-resistant can be a potential source of infection for others. University students living together in crowded conditions increase their risk of acquiring infections. The prevalence of , particularly Methicillin-resistant nasal carriage, in Ethiopian university students is sparse.
OBJECTIVE
This study aimed to determine the nasal carriage rate, associated factors, and antimicrobial susceptibility patterns of methicillin-resistant among pre-clinical students at the College of Health and Medical Sciences, Haramaya University, Ethiopia, from 1 July to 30 August 2022.
METHODS
An institutional-based cross-sectional study was conducted among 270 randomly selected pre-clinical Health and Medical Sciences students. Data on associated factors were collected using pre-tested, structured questionnaires. A nasal swab was taken from each participant and sent to the microbiology laboratory via Amies transport media in a cold chain. There, it was cultivated using conventional techniques. The isolated colonies were found to be , and its antimicrobial susceptibility was performed using the Kirby-Bauer disk diffusion method on Muller-Hinton agar. Methicillin-resistant expressing using cefoxitin based on CLSI breakpoint. Data were entered into Epi-Data version 4.4.2.1 and exported to the Statistical Package for Social Sciences (SPSS) software version 25 for analysis. Pearson's chi-square test was performed to predict the associations between variables. A -value less than 0.05 was regarded as statistically significant.
RESULT
Methicillin-resistant nasal carriage was 5.9% (95% CI: 3.09-8.7) of cases of nasal colonization, which was found to be 12.96% (95% CI: 8.85-16.96). Methicillin-resistant nasal colonization was significantly associated with the history of cigarette smoking ( = 0.000), intake of khat ( = 0.042), nose-picking habit ( = 0.003), history of sharing personal goods ( = 0.021), and history of hospitalizations ( = 0.00). All of the Methicillin-resistant isolates were resistant to ampicillin and cefoxitin.
CONCLUSION
Based on the findings, a considerable proportion of healthy students harbored Methicillin-resistant strains associated with behavioral factors. Furthermore, these isolates showed high resistance to cefoxitin and ampicillin. Hence, it is crucial to regularly test pre-clinical students to prevent endogenous infections and the spread of Methicillin-resistant .
Topics: Humans; Ethiopia; Methicillin-Resistant Staphylococcus aureus; Cross-Sectional Studies; Male; Female; Staphylococcal Infections; Young Adult; Universities; Microbial Sensitivity Tests; Carrier State; Students; Anti-Bacterial Agents; Adult; Adolescent; Prevalence; Risk Factors; Surveys and Questionnaires
PubMed: 38846602
DOI: 10.3389/fpubh.2024.1354461 -
BMC Bioinformatics Jun 2024Bisulfite sequencing (BS-Seq) is a fundamental technique for characterizing DNA methylation profiles. Genotype calling from bisulfite-converted BS-Seq data allows...
BACKGROUND
Bisulfite sequencing (BS-Seq) is a fundamental technique for characterizing DNA methylation profiles. Genotype calling from bisulfite-converted BS-Seq data allows allele-specific methylation analysis and the concurrent exploration of genetic and epigenetic profiles. Despite various methods have been proposed, single nucleotide polymorphisms (SNPs) calling from BS-Seq data, particularly for SNPs on chromosome X and in the presence of contaminative data, poses ongoing challenges.
RESULTS
We introduce bsgenova, a novel SNP caller tailored for bisulfite sequencing data, employing a Bayesian multinomial model. The performance of bsgenova is assessed by comparing SNPs called from real-world BS-Seq data with those from corresponding whole-genome sequencing (WGS) data across three human cell lines. bsgenova is both sensitive and precise, especially for chromosome X, compared with three existing methods. Moreover, in the presence of low-quality reads, bsgenova outperforms other methods notably. In addition, bsgenova is meticulously implemented, leveraging matrix imputation and multi-process parallelization. Compared to existing methods, bsgenova stands out for its speed and efficiency in memory and disk usage. Furthermore, bsgenova integrates bsextractor, a methylation extractor, enhancing its flexibility and expanding its utility.
CONCLUSIONS
We introduce bsgenova for SNP calling from bisulfite-sequencing data. The source code is available at https://github.com/hippo-yf/bsgenova under license GPL-3.0.
Topics: Polymorphism, Single Nucleotide; Humans; DNA Methylation; Sulfites; Sequence Analysis, DNA; Genotype; Software; Whole Genome Sequencing; Bayes Theorem
PubMed: 38840038
DOI: 10.1186/s12859-024-05821-7 -
Veterinary Medicine and Science Jul 2024Ornithobacterium rhinotracheal (ORT) infects numerous birds, particularly chickens and turkeys. ORT is an emerging bacterial pathogen of global concern in the poultry...
BACKGROUND
Ornithobacterium rhinotracheal (ORT) infects numerous birds, particularly chickens and turkeys. ORT is an emerging bacterial pathogen of global concern in the poultry industry. As ORT is rapidly spreading throughout commercial poultry, it requires intensive studies of its epidemiology, diagnostic procedures, molecular typing, virulence genes and antimicrobial resistance.
OBJECTIVES
The present study was conducted in isolation and identification of ORT from slaughtered turkeys.
METHODS
Cleft palate swabs of 200 were collected from slaughtered turkeys and cultured on blood agar. ORT was characterized using biochemical tests and PCR targeting the ORT 16S rRNA gene. Virulence genes of isolates were determined targeting adenylate kinase (adk), copA and virulence-associated protein D (vapD) genes. Additionally, diversity of ORT isolates was performed by enterobacterial repetitive intergenic consensus (ERIC) and RAPD PCR. Disk diffusion was used to determine the antibiotic sensitivity of the isolates.
RESULTS
ORT was identified in 23 (11.5%) samples using both the biochemical tests and PCR. The result of detecting virulence genes showed that all the isolates (23: 100%) had the adk gene, whereas two (8.7%) isolates had the copA gene, and seven (30.43%) isolates had the vapD gene. Molecular typing of isolates revealed 21 different patterns by RAPD PCR assay using M13 primer and 20 distinct patterns by ERIC PCR test. Both ERIC and RAPD PCR were distinctive methods for investigating the genetic diversity of ORT isolates. The antibiotic resistance test showed that 18 (78.26%) isolates were resistant to gentamicin, amikacin, cefazolin, streptomycin and penicillin. All isolates (100%) were resistant to cloxacillin and fosfomycin.
CONCLUSIONS
This study showed the prevalence of ORT in turkey and high resistance of this bacterium to many common veterinary antibiotics. Moreover, both ERIC and RAPD PCR are distinctive methods for investigating the genetic diversity of ORT isolates. These data may help monitor antibiotic resistance and typing of ORT in epidemiological studies and serve as the foundation for designing region-specific vaccines for future use.
Topics: Animals; Turkeys; Poultry Diseases; Ornithobacterium; Flavobacteriaceae Infections; Drug Resistance, Bacterial; Anti-Bacterial Agents
PubMed: 38837675
DOI: 10.1002/vms3.1490 -
Investigative Ophthalmology & Visual... Jun 2024Optical coherence tomography (OCT) representations in clinical practice are static and do not allow for a dynamic visualization and quantification of blood flow. This...
PURPOSE
Optical coherence tomography (OCT) representations in clinical practice are static and do not allow for a dynamic visualization and quantification of blood flow. This study aims to present a method to analyze retinal blood flow dynamics using time-resolved structural OCT.
METHODS
We developed novel imaging protocols to acquire video-rate time-resolved OCT B-scans (1024 × 496 pixels, 10 degrees field of view) at four different sensor integration times (integration time of 44.8 µs at a nominal A-scan rate of 20 kHz, 22.4 µs at 40 kHz, 11.2 µs at 85 kHz, and 7.24 µs at 125 kHz). The vessel centers were manually annotated for each B-scan and surrounding subvolumes were extracted. We used a velocity model based on signal-to-noise ratio (SNR) drops due to fringe washout to calculate blood flow velocity profiles in vessels within five optic disc diameters of the optic disc rim.
RESULTS
Time-resolved dynamic structural OCT revealed pulsatile SNR changes in the analyzed vessels and allowed the calculation of potential blood flow velocities at all integration times. Fringe washout was stronger in acquisitions with longer integration times; however, the ratio of the average SNR to the peak SNR inside the vessel was similar across all integration times.
CONCLUSIONS
We demonstrated the feasibility of estimating blood flow profiles based on fringe washout analysis, showing pulsatile dynamics in vessels close to the optic nerve head using structural OCT. Time-resolved dynamic OCT has the potential to uncover valuable blood flow information in clinical settings.
Topics: Tomography, Optical Coherence; Humans; Retinal Vessels; Blood Flow Velocity; Regional Blood Flow; Optic Disk; Signal-To-Noise Ratio; Male; Female; Adult; Middle Aged
PubMed: 38837167
DOI: 10.1167/iovs.65.6.9 -
Canada Communicable Disease Report =... May 2024Invasive group A streptococcal (iGAS, ) disease has been a nationally notifiable disease in Canada since 2000. This report summarizes the demographics, types, and...
BACKGROUND
Invasive group A streptococcal (iGAS, ) disease has been a nationally notifiable disease in Canada since 2000. This report summarizes the demographics, types, and antimicrobial resistance of iGAS isolates collected in Canada in 2021 and 2022.
METHODS
The Public Health Agency of Canada's National Microbiology Laboratory collaborates with provincial and territorial public health laboratories to conduct national surveillance of invasive . typing was performed using the Centers for Disease Control and Prevention sequencing protocol or extracted from whole-genome sequencing data. Antimicrobial susceptibilities were determined using Kirby-Bauer disk diffusion according to Clinical and Laboratory Standards Institute guidelines or predicted from whole-genome sequencing data based on the presence of resistance determinants.
RESULTS
Overall, the incidence of iGAS disease in Canada was 5.56 cases per 100,000 population in 2021, decreasing from the peak of 8.6 cases per 100,000 population in 2018. A total of 2,630 iGAS isolates were collected during 2022, representing an increase from 2021 (n=2,179). In particular, there was a large increase in isolates collected from October to December 2022. The most predominant type overall in 2021 and 2022 was 49, at 21.5% (n=468) and 16.9% (n=444), respectively, representing a significant increase in prevalence since 2018 (<0.0001). The former most prevalent type, 1, increased from 0.5% (n=10) in 2021 to 4.8% (n=125) in 2022; similarly, 12 increased from 1.0% (n=22) in 2021 to 5.8% (n=151) in 2022. These two types together accounted for almost 25% of isolates collected in late 2022 (October to December). Antimicrobial resistance rates in 2021 and 2022 included: 14.9%/14.1% erythromycin resistance, 4.8%/3.0% clindamycin resistance, and <1% chloramphenicol resistance.
CONCLUSION
The increase of iGAS isolates collected in Canada is an important public health concern. Continued surveillance of iGAS is critical to monitor expanding types and antimicrobial resistance patterns.
PubMed: 38835501
DOI: 10.14745/ccdr.v50i05a03 -
Scientific Reports Jun 2024This study reports the antibacterial and antibiofilm activities of Magnesium ferrite nanoparticles (MgFeO) against gram-positive and gram-negative bacteria. The...
This study reports the antibacterial and antibiofilm activities of Magnesium ferrite nanoparticles (MgFeO) against gram-positive and gram-negative bacteria. The photocatalytic degradation of Carbol Fuchsin (CF) dye (a class of dyestuffs that are resistant to biodegradation) under the influence of UV-light irradiation is also studied. The crystalline magnesium ferrite (MgFeO) nanoparticles were synthesized using the co-precipitation method. The morphology of the resulting nanocomposite was examined using scanning electron microscopy (SEM), while transmission electron microscopy (TEM) was employed for further characterization of particle morphology and size. Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) were utilized to analyze the crystalline structure, chemical composition, and surface area, respectively. Optical properties were evaluated using UV-Vis spectroscopy. The UV-assisted photocatalytic performance of MgFeO nanoparticles was assessed by studying the decolorization of Carbol fuchsin (CF) azo dye. The crystallite size of the MgFeO nanoparticles at the (311) plane, the most prominent peak, was determined to be 28.5 nm. The photocatalytic degradation of 10 ppm CF using 15 mg of MgFeO nanoparticles resulted in a significant 96% reduction after 135 min at ambient temperature (25 °C) and a pH value of 9. Additionally, MgFeO nanoparticles exhibited potent antibacterial activity against E. coli and S. aureus in a dose dependent manner with maximum utilized concentration of 30 µg/ml. Specifically, MgFeO nanoparticles demonstrated substantial antibacterial activity via disk diffusion and microbroth dilution tests with zones of inhibition and minimum inhibitory concentrations (MIC) for E. coli (26.0 mm, 1.25 µg/ml) and S. aureus (23.0 mm, 2.5 µg/ml), respectively. Moreover, 10.0 µg/ml of MgFeO nanoparticles elicited marked percent reduction in biofilm formation by E. coli (89%) followed by S. aureus (78.5%) after treatment. In conclusion, MgFeO nanoparticles demonstrated efficient dye removal capabilities along with significant antimicrobial and antibiofilm activity against gram-positive and gram-negative bacterial strains suggesting their potential as promising antimicrobial and detoxifying agents.
Topics: Biofilms; Ferric Compounds; Catalysis; Magnetite Nanoparticles; Anti-Bacterial Agents; Microbial Sensitivity Tests; Escherichia coli; Ultraviolet Rays; Staphylococcus aureus; Magnesium; Spectroscopy, Fourier Transform Infrared
PubMed: 38834648
DOI: 10.1038/s41598-024-62868-5 -
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