Bacterial Culture Research Articles

Assessing the Predictive Value of Methicillin-Resistant Staphylococcus aureus Nares Colonization Among Transplant Recipients and Patients With Neutropenia.

Methicillin-resistant Staphylococcus aureus (MRSA) nares screening has been shown to be a powerful antibiotic stewardship tool for MRSA infections within 7 days of screening across a variety of anatomical locations given the high negative predictive value (NPV). However, the utility outside of 7 days and among transplant recipients and patients with neutropenia is less clear. This was a retrospective cohort study across Veterans Affairs medical centers in the United States from 1 January 2007 to 1 January 2023 of patients tested for MRSA colonization and who had a subsequent positive bacterial culture within 28 days of MRSA sc---reening. Sensitivity, specificity, positive predictive value, and NPV were calculated across different time points and anatomical culture locations. The cohort consisted of 686 174 patients, 6 277 437 MRSA nares tests, and 2 446 766 positive bacterial cultures within 28 days of MRSA testing. The NPV of MRSA nares screening for ruling out a MRSA infection within 28 days was 95.8% across all anatomical culture sites. The NPV was 97.9% among patients with neutropenia and 97.5% in solid organ and hemopoietic stem cell transplant recipients. MRSA nares screening can reliably be used for de-escalation of anti-MRSA therapy within 28 days of bacterial culture for all patients, including solid organ and hematopoietic transplant recipients and patients with neutropenia.

The characteristics of autolysins associated with cell separation in Bacillus subtilis.

The peptidoglycan hydrolases responsible for the cell separation of Bacillus subtilis cells are collectively referred to as autolysins. However, the role of each autolysin in the cell separation of B. subtilis is not fully understood. In this study, we constructed a series of cell separation-associated autolysin deficient strains and strains overexpressing the transcription factors SlrR and SinR, and the morphological changes of these strains in liquid culture were observed. The results showed that the absence of D,L-endopeptidases CwlS and LytF only increased the cell chain length in the early exponential phase. The absence of D,L-endopeptidase LytE or N-acetylmuramyl-L-alanine amidase LytC can cause cells to form chains throughout the growth of B. subtilis, although the cell chain length was significantly shortened during the stationary phase. However, the absence of peptidoglycan N-acetylglucosaminidase LytD only caused minor defect in cell separation. Therefore, we concluded that LytE and LytC were the major autolysins that ensure the timely separation of B. subtilis daughter cells, whereas CwlS, LytF, and LytD were the minor autolysins. In addition, overexpression of the transcription factors SinR and SlrR in the cwlS lytF lytC lytE mutant enabled B. subtilis cells to form ultra-long chains in the vegetative phase, and its biomass level was basically the same as that of the wild type. This led to the conclusion that besides inhibiting the expression of lytC and lytF, the SinR-SlrR complex also has other potential mechanisms to inhibit cell separation.IMPORTANCEIn this study, the effects of CwlS, LytC, LytD, LytF, LytE, and SinR-SlrR complex on the cell separation of Bacillus subtilis at different growth phases were studied, and an ultra-long-chained B. subtilis strain was constructed. In microbial fermentation, due to its large cell size, this ultra-long-chained B. subtilis strain may be more likely to be precipitated or intercepted during the removal of bacterial process with centrifugation and membrane filtration as the main methods, which is crucial to improve the purity of the product.

Lecanicillium psalliotae (Hypocreales: Cordycipitaceae) Exerts Ovicidal and Larvicidal Effects against the Sheep Blood-Feeding Nematode Haemonchus contortus through Its Liquid Culture Filtrates.

Nematophagous fungi (NF) form part of the soil microbiota and are natural enemies of nematodes, helping to regulate nematode populations. A verticillate NF isolated from soil from Tepalcingo, Mexico, was morphologically and molecularly characterised. This fungus was cultured in two different liquid media-Czapek-Dox broth (CzDoxB) and sweet potato dextrose broth (SPDB)-for 21 days. The ovicidal (OA) and larvicidal (LA) activities of fungal liquid culture filtrates (LCFs) were assessed in 96-well microtitre plates at different concentrations against Haemonchus contortus after 48 h. The morphological and molecular identification revealed the presence of Lecanicillium psalliotae. Additionally, the groups of compounds associated with nematocidal activity were determined from a qualitative chemical profile (QCP) using different reagents. The highest OA of the LCFs was obtained at 25 mg/mL from SPDB and CzDoxB and amounted to 97.2 and 99.06%, respectively. Meanwhile, the highest LA recorded with these LCFs at 100 mg/mL was 54.27% and 96.8%, respectively. The QCP revealed the presence of alkaloids and tannins in both LCFs that have previously been associated with nematocidal activity. Lecanicillium psalliotae exerted an important effect on H. contortus and could be of significance in future studies focused on the control and prevention of haemonchosis in small ruminants.

Study on the Biological Characteristics of Dark Septate Endophytes under Drought and Cadmium Stress and Their Effects on Regulating the Stress Resistance of Astragalus membranaceus.

Astragalus membranaceus is a famous traditional medicinal plant. However, drought and cadmium (Cd) pollution are the main abiotic stress factors that affect plant growth and yield and the ability to improve the host's stress resistance through the use of beneficial endophytic fungi. To evaluate the tolerance of dark septate endophytes (DSE) to various abiotic stresses, 10 DSE strains [Microsphaeropsis cytisi (Mc), Alternaria alstroemeriae (Aa), Stagonosporopsis lupini (Sl), Neocamarosporium phragmitis (Np), Paraphoma chlamydocopiosa (Pc), Macrophomina phaseolina (Mp'), Papulaspora equi (Pe), Alternaria tellustris (At), Macrophomina pseudophaseolina (Mp), and Paraphoma radicina (Pr)] were investigated under different drought and Cd stressors in vitro by using solid-plate cultures and liquid-shaker cultures in the current study. The experiments involved using varying concentrations of PEG (0, 9, 18, and 27%) and Cd2+ (0, 25, 50, and 100 mg/L) to simulate different stress conditions on DSE. Additionally, the effect of DSE (Np and At) on the growth of A. membranaceus at different field water capacities (70% and 40%) and at different CdCl2 concentrations (0, 5, 10, and 15 mg Cd/kg) in soil was studied. The results demonstrated that the colony growth rates of Aa, Np, Pc, Mp', and Mp were the first to reach the maximum diameter at a PEG concentration of 18%. Aa, Np, and At remained growth-active at 100 mg Cd/L. In addition, Aa, Np, and At were selected for drought and Cd stress tests. The results of the drought-combined-with-Cd-stress solid culture indicated that the growth rate of Np was significantly superior to that of the other strains. In the liquid culture condition, the biomasses of Np and Aa were the highest, with biomasses of 1.39 g and 1.23 g under the concentration of 18% + 25 mg Cd/L, and At had the highest biomass of 1.71 g at 18% + 50 mg Cd/L concentration, respectively. The CAT and POD activities of Np reached their peak levels at concentrations of 27% + 50 mg Cd/L and 27% + 25 mg Cd/L, respectively. Compared to the control, these levels indicated increases of 416.97% and 573.12%, respectively. Aa, Np, and At positively influenced SOD activity. The glutathione (GSH) contents of Aa, Np, and At were increased under different combined stressors of drought and Cd. The structural-equation-modeling (SEM) analysis revealed that Aa positively influenced biomass and negatively affected Cd content, while Np and At positively influenced Cd content. Under the stress of 40% field-water capacity and the synergistic stress of 40% field-water capacity and 5 mg Cd/kg soil, Np and At significantly increased root weight of A. membranaceus. This study provides guidance for the establishment of agricultural planting systems and has good development and utilization value.

Arthrobotrys oligospora (Fungi: Orbiliales) and its liquid culture filtrate myco-constituents kill Haemonchus contortus infective larvae (Nematoda: trichostrongylidae)

ABSTRACT Arthrobotrys oligospora is a nematode-trapping fungus belonging to the family Orbiliaceae and one of the main antagonists of nematodes in soil, including plant and animal parasitic nematodes and free-living nematodes. This species develops three-dimensional adhesive nets in which nematodes are trapped, destroyed and consumed by the fungus. It also possesses other strategies to immobilise, kill and degrade nematodes, i.e. nematode-attractant substances, cuticle adhesion polymers and a number of nematocidal metabolites. The objective of this study was to assess the in vitro nematocidal activity of a strain of A. oligospora through its predatory activity and its liquid culture filtrates (LCF) against the ruminant parasite Haemonchus contortus (HcL3) and to investigate the presence of myco-compounds with potential nematocidal activity. Predatory activity (PA) was assessed in agar plates; 200 HcL3 were placed on agar plates with the fungus and a control group and incubated for 10 days. The LCF confrontation with nematodes was performed in microtiter plates. Two media, Czapek-Dox Broth (Cz-DB) and potato dextrose broth, were assessed. Three concentrations (25, 50 and 100 mg/mL) were assessed at 48 and 72 h (n = 4, per concentration). The experiment was performed in triplicate. The results showed 73.6 ± 2.7% PA and the highest mortality (83%) with the LCF in Cz-DB after 72 h. Gas chromatography–mass spectrometry (GC–MS) analysis revealed that the A. oligospora ethyl acetate phase was composed of 1,2-benzenedicarboxylic acid, bis (2-methylpropyl) ester, (M) 1,4-benzenedicarboxylic acid, bis (2-methylpropyl) ester and (M) decanedioic acid (2-ethylexyl) ester. These compounds could be responsible for nematocidal activity.

Molecular methods enhance the detection of pyoderma-related Streptococcus pyogenes and emm-type distribution in children.

Streptococcus pyogenes-related skin infections are increasingly implicated in the development of rheumatic heart disease (RHD) in lower-resourced settings, where they are often associated with scabies. The true prevalence of S. pyogenes-related pyoderma may be underestimated by bacterial culture. A multiplex qPCR for S. pyogenes, Staphylococcus aureus and Sarcoptes scabiei was applied to 250 pyoderma swabs from a cross-sectional study of children <5 years in The Gambia. Direct PCR-based emm-typing was used to supplement previous whole genome sequencing (WGS) of cultured isolates. Pyoderma lesions with S. pyogenes increased from 51% (127/250) using culture to 80% (199/250) with qPCR. Compared to qPCR, the sensitivity of culture was 95.4% for S. pyogenes (95% CI 77.2-99.9) in samples with S. pyogenes alone (22/250, 9%), but 59.9% (95% CI 52.3-67.2) for samples with S. aureus co-infection (177/250, 71%). Direct PCR-based emm-typing was successful in 50% (46/92) of cases, identifying 27 emm-types, including six not identified by WGS (total 52 emm-types). Bacterial culture significantly underestimates the burden of S. pyogenes in pyoderma, particularly when co-infected with S. aureus. Molecular methods should be used to enhance the detection of S. pyogenes in surveillance studies and clinical trials of preventative measures in RHD-endemic settings.

An updated description of bacterial pneumonia in adult horses and factors associated with death.

Available descriptive studies on equine pneumonia are outdated or focus on specific horse or bacterial populations. To describe the clinical presentation and bacterial isolates of adult horses with bacterial pneumonia and identify factors associated with death. One hundred sixteen horses >2 years old with bacterial pneumonia. Retrospective case series. Data regarding history, physical examination, clinicopathologic features, treatment, bacterial culture and sensitivity, and outcome were collected and analyzed retrospectively. Historical risk factors were present for 60% of cases, whereas abnormal vital signs on intake were present for <50%. Most horses (58%) underwent at least 1 change of antimicrobial treatment, and 67% received the highest-priority critically important antimicrobials. Streptococcus zooepidemicus was the most isolated bacteria (44%), followed by Escherichia coli (19%), Klebsiella spp. (18%), other Streptococcus species (17%), and Bacillus spp. (13%). Fusobacterium spp. were the most common anaerobic isolates (11%). Antimicrobial susceptibility varied widely. Survival to discharge was 73%. Heart rate at presentation (odds ratio [OR] 1.08, 95% confidence interval [CI] 1.008-1.17, P = .03) and higher creatinine (OR 14.1, 95% CI 1.56-127.6, P = .02) increased the risk of death. Higher lymphocyte count (OR 0.27, 95% CI 0.08-0.94, P = .04) reduced risk. Contrasting older literature, Fusobacterium spp. were the most common anaerobes. Streptococcus zooepidemicus remained the most common isolate and was predictably susceptible to penicillin. Antimicrobial susceptibility was otherwise variable and broad applicability is limited as this was a single-center study. Increased risk of death associated with tachycardia and abnormally high serum creatinine concentration is consistent with previous studies.

Duffy Antigen Receptor for Chemokines (DARC) Nanodisc-Based Biosensor for Detection of Staphylococcal Bicomponent Pore-Forming Leukocidins.

Staphylococcus aureus (S. aureus) is an opportunistic infectious pathogen, which causes a high mortality rate during bloodstream infections. The early detection of virulent strains in patients' blood samples is of medical interest for rapid diagnosis. The main virulent factors identified in patient isolates include leukocidins that bind to specific membrane receptors and lyse immune cells and erythrocytes. Duffy antigen receptor for chemokines (DARC) on the surface of specific cells is a main target of leukocidins such as gamma-hemolysin AB (HlgAB) and leukocidin ED (LukED). Among them, HlgAB is a conserved and critical leukocidin that binds to DARC and forms pores on the cell membranes, leading to cell lysis. Current methods are based on ELISA or bacterial culture, which takes hours to days. For detecting HlgAB with faster response and higher sensitivity, we developed a biosensor that combines single-walled carbon nanotube field effect transistors (swCNT-FETs) with immobilized DARC receptors as biosensing elements. DARC was purified from a bacterial expression system and successfully reconstituted into nanodiscs that preserve binding capability for HlgAB. Dynamic light scattering (DLS) and scanning electron microscopy (SEM) showed an increase of the DARC-containing nanodisc size in the presence of HlgAB, indicating the formation of HlgAB prepore or pore complexes. We demonstrate that this sensor can specifically detect the leukocidins HlgA and HlgAB in a quantitative manner within the dynamic range of 1 fM to 100 pM with an LOD of 0.122 fM and an LOQ of 0.441 fM. The sensor was challenged with human serum spiked with HlgAB as simulated clinical samples. After dilution for decreasing nonspecific binding, it selectively detected the toxin with a similar detection range and apparent dissociation constant as in the buffer. This biosensor was demonstrated with remarkable sensitivity to detect HlgAB rapidly and has the potential as a tool for fundamental research and clinical applications, although this sensor cannot differentiate between HlgAB and LukED as both have the same receptor.

Absence of effects of widespread badger culling on tuberculosis in cattle

Government policy in England aims for the elimination of bovine tuberculosis (bTB). This policy includes culling of European badger (Meles meles) to reduce cattle TB incidence. The rationale is based on a field trial, the Randomised Badger Culling Trial (RBCT) 1998–2005, which reported a substantial decrease in bTB herd incidence where badger culling had been implemented, in comparison to untreated control areas. The RBCT was undertaken because previous studies of reductions in badgers by culling, reported a possible association between bTB in badger and cattle, but none could directly show causation. The effect of intensive widespread (proactive) culling in the RBCT was reported in 2006 in the journal Nature. Analysis of an extensive badger removal programme in England since 2013 has raised concerns that culling has not reduced bTB herd incidence. The present study re-examined RBCT data using a range of statistical models. Most analytical options showed no evidence to support an effect of badger culling on bTB herd incidence ‘confirmed’ by visible lesions and/or bacterial culture post mortem following a comparative intradermal skin test (SICCT). However, the statistical model chosen by the RBCT study was one of the few models that showed an effect. Various criteria suggest that this was not an optimal model, compared to other analytical options available. The most likely explanation is that the RBCT proactive cull analysis over-fitted the data with a non-standard method to control for exposure giving it a poor predictive value. Fresh appraisal shows that there was insufficient evidence to conclude RBCT proactive badger culling affected bTB breakdown incidence. The RBCT found no evidence of an effect of culling on ‘total’ herd incidence rates. Total herd incidences include those confirmed as bTB at necropsy and those herds where there was at least one animal animal positive to the comparative intradermal skin test, the standard diagnostic test used for routine surveillance, but not confirmed at necropsy. This was also the case using the more suitable statistical models. Use only of ‘confirmed’ herd incidence data, together with a more recent (2013) published perception that RBCT data presented ‘a strong evidence base….with appropriate detailed statistical or other quantitative analysis’ should be reconsidered. The results of the present report are consistent with other analyses that were unable to detect any disease control benefits from badger culling in England (2013–2019). This study demonstrates one form of potential driver to the reproducibility crisis, in this case with disease control management in an increasingly intensified livestock industry.

Prevalence And Pattern Sensitivity Multidrug Antibiotics Resistant Pseudomonas aeruginosa in the High Care Unit at Dr. Soetomo General Academic Hospital Period 2022-2023

The prevalence of Multidrug antibiotic-resistant Pseudomonas aeruginosa (MDRPA) has been increasing during the decade And has become attention in hospital patients. This retrospective descriptive descriptive aimed to determine the prevalence of MDRPA and its sensitivity patterns. Data were taken from results of bacterial culture and antibiotic resistance tests from various clinical specimens from patients at Dr. Soetomo General Academic Hospital throughout 2022-2023. The resistance test was carried out using a Vitek 2 compact instrument. MDRPA is defined as Pseudomonas aeruginosa that is not sensitive to three or more of the following classes of antibiotics: meropenem or imipenem, ciprofloxacin, gentamicin or amikacin, ceftazidime or cefepime, and piperacillin/ tazobactam. The prevalence of MDRPA was 57.0%. MDRPA isolates were also the most common origin from the burn unit and HCU A (high care unit A), mostly from pus specimens and sputum. Pseudomonas aeruginosa sensitivity was best with piperacillin/tazobactam (55.5%), meropenem (54.8%), amikacin (47.5%), gentamicin (46.5%), cefepime (46.3%), ceftazidime (45.0%), ciprofloxacin (44.7%) and aztreonam (43.2%). The sensitivity of MDRPA to antibiotics is much lower than that of Pseudomonas aeruginosa. This study showed high number of MDRPA specifically in Surabaya and the pattern sensitivity of Pseudomonas aeruginosa can become guidelines in choosing antibiotics treatment for patients.

Immobilized recombinant laccase over PEGylated silica-coated magnetic nanoparticles for anti-inflammatory modulation in pro-monocytic model cell line

This study aimed to develop a nano-biosystem by covalently binding recombinant laccase from Bacillus licheniformis (rLACBL) to PEGylated silica-coated magnetic nanoparticles (EMNPs-PEG) and evaluate its cytotoxicity and anti-inflammatory properties on a pro-monocytic cell line. The active rLACBL was purified from the bacterial culture with a yield of approximately 14 mg/L and purity of about 91 %. The physicochemical characteristics of EMNP-PEG-rLACBL were confirmed using DLS, UV-Vis spectrum, FTIR, EDS, and SEM. The immobilized rLACBL exhibited improved kinetic parameters compared to the bare enzyme. The IC50 value for EMNP-PEG-rLACBL (58.7 μg/mL) was lower than that of the bare enzyme after 48 hours of treatment on U937 cells. Both EMNP-PEG-rLACBL and rLACBL significantly decreased the expression levels of key cytokines (TNF-α, IL-6, IL-17, and IL-23) in LPS-stimulated cells, indicating promising anti-inflammatory properties of rLACBL. Given the association between chronic inflammation and cancer, this newly developed enzyme-based nanobiomedicine holds potential as a therapeutic option for inflammatory conditions and malignant diseases. However, further research is needed to validate these findings and fully assess the therapeutic potential of LACs before clinical translation can be considered.

Brain Abscesses in Domestic Ruminants: Clinicopathological and Bacteriological Approaches.

Brain abscesses in ruminants often arise from primary infection foci, leading to an unfavorable prognosis for affected animals. This highlights the need for comprehensive studies on brain abscesses across different ruminant species. We retrospectively investigated medical records of epidemiological, clinical, neuroimaging, anatomopathological, and bacteriological findings in six ruminants (three goats, two cows, and one sheep) diagnosed with brain abscesses. All animals studied were female. Apathy (50%), compulsive walking (33%), decreased facial sensitivity (33%), head pressing (33%), seizures (33%), semicomatous mental status (33%), strabismus (33%), unilateral blindness (33%), and circling (33%) represented the most common neurologic signs. Leukocytosis and neutrophilia were the main findings in the hematological evaluation. Cerebrospinal fluid (CSF) analysis revealed predominant hyperproteinorrachia and pleocytosis. In three cases, computed tomography or magnetic resonance imaging were used, enabling the identification of typical abscess lesions, which were subsequently confirmed during postmortem examination. Microbiological culture of the abscess samples and/or CSF revealed bacterial coinfections in most cases. Advanced imaging examinations, combined with CSF analysis, can aid in diagnosis, although confirmation typically relies on postmortem evaluation and isolation of the causative agent. This study contributes to clinicopathological aspects, neuroimages, and bacteriological diagnosis of brain abscesses in domestic ruminants.

Efficacy and safety of topical azithromycin therapy in patients with blepharitis and meibomian gland dysfunction.

To assess the effects of 1% azithromycin ophthalmic solution (AZM) in patients with bacterial blepharitis accompanied by meibomian gland dysfunction (MGD). A multicenter, single arm, prospective interventional study. AZM was administered to the affected eyes twice daily for the first 2 days and once daily for the subsequent 12 days. Lid margin hyperaemia/redness, collarette at the root of the eyelashes, conjunctival hyperaemia, foreign body sensation, and epiphora were assessed on Days 1, 14, and 28. The Dry Eye-related Quality of Life Score (DEQS) and objectives related to MGD, including lid vascularity, lid margin irregularity, foaming, lid plugging, keratoconjunctival disorders, Marx line, meibum grade, and tear breakup time, were also assessed. Bacterial culture of the conjunctival sac and meibum was performed on Days 1 and 14. Twenty-four eyes of 24 patients (10 men/14 women, mean age 72.3 ± 13.2) were included. On Days 14 and 28, the total score, lid vascularity, lid plugging, and meibum grade showed significant improvement (p < 0.05). On Day 1, 71 strains were isolated from 22 of the 24 eyes (91.7%). Cutibacterium acnes, Corynebacterium spp., and Staphylococci were detected at high frequencies. The overall disappearance rates of the bacteria in the conjunctival sac and meibum at the end of treatment were 65.7% and 58.3%, respectively. No serious ocular or systemic adverse events were observed. Fourteen-day treatment with AZM was effective in patients with blepharitis accompanied by MGD, and the efficacy of AZM persisted for a period after the treatment.

Previously unknown regulatory role of extracellular RNA on bacterial directional migration.

Bacterial directional migration plays a significant role in bacterial adaptation. However, the regulation of this process, particularly in young biofilms, remains unclear. Here, we demonstrated the critical role of extracellular RNA as part of the Universal Receptive System in bacterial directional migration using a multidisciplinary approach, including bacterial culture, biochemistry, and genetics. We found that the destruction or inactivation of extracellular RNA with RNase or RNA-specific antibodies in the presence of the chemoattractant triggered the formation of bacterial "runner cells» in what we call a "panic state" capable of directional migration. These cells quickly migrated even on the surface of 1.5% agar and formed evolved colonies that were transcriptionally and biochemically different from the ancestral cells. We have also shown that cell-free DNA from blood plasma can act as a potent bacterial chemoattractant. Our data revealed a previously unknown role of bacterial extracellular RNA in the regulation of bacterial migration and have shown that its destruction or inhibition triggered the directional migration of developing and mature biofilms towards the chemoattractant.

Growing Mycobacterial Biofilm as a Model to Study Antimicrobial Resistance.

Many bacteria thrive in intricate natural communities, exhibiting key attributes of multicellularity such as communication, cooperation, and competition. The most prevalent manifestation of bacterial multicellular behavior is the formation of biofilms, often linked to pathogenicity. Biofilms offer a haven against antimicrobial agents, fostering the emergence of antimicrobial resistance. The conventional practice of cultivating bacteria in shake flask liquid cultures fails to represent their proper physiological growth in nature, consequently limiting our comprehension of their intricate dynamics. Notably, the metabolic and transcriptional profiles of bacteria residing in biofilms closely resemble those of naturally growing cells. This parallelism underscores the significance of biofilms as an ideal model for foundational and translational research. This article focuses on utilizing Mycobacterium smegmatis as a model organism to illustrate a technique for cultivating pellicle biofilms. The approach is adaptable to various culture volumes, facilitating its implementation for diverse experimental objectives such as antimicrobial studies. Moreover, the method's design enables the qualitative or quantitative evaluation of the biofilm-forming capabilities of different mycobacterial species with minor adjustments.

A colorimetric biosensor with infrared sterilization based on CuSe nanoparticles for the detection of E. coli O157:H7 in food samples.

Escherichia coli O157:H7 is a major threat to public health. At present, the detection methods for E. coli O157:H7 mainly include traditional bacterial culture, immunology (enzyme-linked immune-sorbent assay) and molecular biology techniques (polymerase chain reaction). These methods have the limitations of professional operation, waste of time and energy, and high cost. Therefore, we have developed a simple, fast, bactericidal colorimetric biosensor to detect E. coli. O157:H7. The entire process was completed in 80 minutes. The method has been successfully applied to milk and mineral water samples with satisfactory results, proving that the method is an effective method for real-time detection and inactivation of bacteria.

Herbidomicins, two pairs of polyketide tautomers produced by an actinomycete of the genus Herbidospora.

Herbidospora is one of the underexplored actinomycete genera from which only a limited number of secondary metabolites are reported. In our continuing investigation on less explored actinomycetes, a liquid culture of Herbidospora sp. RD 11066 was found to contain unknown metabolites that had no match in our in-house UV database. Chromatographic separation and following structural analysis using NMR and MS identified these metabolites to be chromanone and chromene derivatives, which were respectively composed of an inseparable mixture of two isomeric forms. The former polyketides, designated to be herbidomicins A1 (1) and A2 (2), are positional isomers in terms of a methyl substituent on an aromatic ring that mutually interconvert by acetal exchange by two phenolic hydroxy groups. The latter pair, herbidomicins B1 (3) and B2 (4), is Z/E-isomers regarding an enol ether double bond. Herbidomicins 1-4 were weakly antifungal against a dermatophytic fungus Trichophyton rubrum and were moderately cytotoxic against murine leukemia P388 cells.

Predictive Model for Extended-Spectrum β-Lactamase-Producing Bacterial Infections Using Natural Language Processing Technique and Open Data in Intensive Care Unit Environment: Retrospective Observational Study.

Machine learning has advanced medical event prediction, mostly using private data. The public MIMIC-3 (Medical Information Mart for Intensive Care III) data set, which contains detailed data on over 40,000 intensive care unit patients, stands out as it can help develop better models including structured and textual data. This study aimed to build and test a machine learning model using the MIMIC-3 data set to determine the effectiveness of information extracted from electronic medical record text using a named entity recognition, specifically QuickUMLS, for predicting important medical events. Using the prediction of extended-spectrum β-lactamase (ESBL)-producing bacterial infections as an example, this study shows how open data sources and simple technology can be useful for making clinically meaningful predictions. The MIMIC-3 data set, including demographics, vital signs, laboratory results, and textual data, such as discharge summaries, was used. This study specifically targeted patients diagnosed with Klebsiella pneumoniae or Escherichia coli infection. Predictions were based on ESBL-producing bacterial standards and the minimum inhibitory concentration criteria. Both the structured data and extracted patient histories were used as predictors. In total, 2 models, an L1-regularized logistic regression model and a LightGBM model, were evaluated using the receiver operating characteristic area under the curve (ROC-AUC) and the precision-recall curve area under the curve (PR-AUC). Of 46,520 MIMIC-3 patients, 4046 were identified with bacterial cultures, indicating the presence of K pneumoniae or E coli. After excluding patients who lacked discharge summary text, 3614 patients remained. The L1-penalized model, with variables from only the structured data, displayed a ROC-AUC of 0.646 and a PR-AUC of 0.307. The LightGBM model, combining structured and textual data, achieved a ROC-AUC of 0.707 and a PR-AUC of 0.369. Key contributors to the LightGBM model included patient age, duration since hospital admission, and specific medical history such as diabetes. The structured data-based model showed improved performance compared to the reference models. Performance was further improved when textual medical history was included. Compared to other models predicting drug-resistant bacteria, the results of this study ranked in the middle. Some misidentifications, potentially due to the limitations of QuickUMLS, may have affected the accuracy of the model. This study successfully developed a predictive model for ESBL-producing bacterial infections using the MIMIC-3 data set, yielding results consistent with existing literature. This model stands out for its transparency and reliance on open data and open-named entity recognition technology. The performance of the model was enhanced using textual information. With advancements in natural language processing tools such as BERT and GPT, the extraction of medical data from text holds substantial potential for future model optimization.

Predictive Model for Extended-Spectrum β-Lactamase-Producing Bacterial Infections Using Natural Language Processing Technique and Open Data in Intensive Care Unit Environment: Retrospective Observational Study.

Machine learning has advanced medical event prediction, mostly using private data. The public MIMIC-3 (Medical Information Mart for Intensive Care III) data set, which contains detailed data on over 40,000 intensive care unit patients, stands out as it can help develop better models including structured and textual data. This study aimed to build and test a machine learning model using the MIMIC-3 data set to determine the effectiveness of information extracted from electronic medical record text using a named entity recognition, specifically QuickUMLS, for predicting important medical events. Using the prediction of extended-spectrum β-lactamase (ESBL)-producing bacterial infections as an example, this study shows how open data sources and simple technology can be useful for making clinically meaningful predictions. The MIMIC-3 data set, including demographics, vital signs, laboratory results, and textual data, such as discharge summaries, was used. This study specifically targeted patients diagnosed with Klebsiella pneumoniae or Escherichia coli infection. Predictions were based on ESBL-producing bacterial standards and the minimum inhibitory concentration criteria. Both the structured data and extracted patient histories were used as predictors. In total, 2 models, an L1-regularized logistic regression model and a LightGBM model, were evaluated using the receiver operating characteristic area under the curve (ROC-AUC) and the precision-recall curve area under the curve (PR-AUC). Of 46,520 MIMIC-3 patients, 4046 were identified with bacterial cultures, indicating the presence of K pneumoniae or E coli. After excluding patients who lacked discharge summary text, 3614 patients remained. The L1-penalized model, with variables from only the structured data, displayed a ROC-AUC of 0.646 and a PR-AUC of 0.307. The LightGBM model, combining structured and textual data, achieved a ROC-AUC of 0.707 and a PR-AUC of 0.369. Key contributors to the LightGBM model included patient age, duration since hospital admission, and specific medical history such as diabetes. The structured data-based model showed improved performance compared to the reference models. Performance was further improved when textual medical history was included. Compared to other models predicting drug-resistant bacteria, the results of this study ranked in the middle. Some misidentifications, potentially due to the limitations of QuickUMLS, may have affected the accuracy of the model. This study successfully developed a predictive model for ESBL-producing bacterial infections using the MIMIC-3 data set, yielding results consistent with existing literature. This model stands out for its transparency and reliance on open data and open-named entity recognition technology. The performance of the model was enhanced using textual information. With advancements in natural language processing tools such as BERT and GPT, the extraction of medical data from text holds substantial potential for future model optimization.

Digital PCR assay for the specific detection and estimation of Salmonella contamination levels in poultry rinse

Strains of Salmonella are a frequent cause of foodborne illness and are known to contaminate poultry products. Most Salmonella testing methods can qualitatively detect Salmonella and cannot quantify or estimate the Salmonella load in samples. Therefore, the aim of this study was to standardize and validate a partitioned-based digital PCR (dPCR) assay for the detection and estimation of Salmonella contamination levels in poultry rinses. Pure culture Salmonella strains were cultured, enumerated, cold-stressed for 48 h, and used to inoculate whole carcass chicken rinse (WCCR) at 1–4 log CFU/30 mL and enriched at 37 °C for 5 h. Undiluted DNA samples with primer and probes targeting the Salmonella-specific invA gene were used for the dPCR assay. The dPCR assay was highly specific, with a limit of detection of 0.001 ng/μL and a limit of quantification of 0.01 ng/μL. The dPCR assay further showed no PCR reaction inhibition up to 5 μg of crude DNA extract. The assays accurately detected all cold-stressed Salmonella in inoculated WCCR samples following a 5-h enrichment. Most importantly, when converted to log, the dPCR copies/μL values accurately estimated the inoculated Salmonella levels. The dPCR assay standardized in this study is a robust method for the detection and estimation of Salmonella concentration in contaminated food samples. This approach can allow same-day decision-making for poultry processors attempting to maintain limits and controls on Salmonella contamination.