Identification Of Microorganisms Research Articles

Lighting the Path: Raman Spectroscopy’s Journey Through the Microbial Maze

The rapid and precise identification of microorganisms is essential in environmental science, pharmaceuticals, food safety, and medical diagnostics. Raman spectroscopy, valued for its ability to provide detailed chemical and structural information, has gained significant traction in these fields, especially with the adoption of various excitation wavelengths and tailored optical setups. The choice of wavelength and setup in Raman spectroscopy is influenced by factors such as applicability, cost, and whether bulk or single-cell analysis is performed, each impacting sensitivity and specificity in bacterial detection. In this study, we investigate the potential of different excitation wavelengths for bacterial identification, utilizing a mock culture composed of six bacterial species: three Gram-positive (S. warneri, S. cohnii, and E. malodoratus) and three Gram-negative (P. stutzeri, K. terrigena, and E. coli). To improve bacterial classification, we applied machine learning models to analyze and extract unique spectral features from Raman data. The results indicate that the choice of excitation wavelength significantly influences the bacterial spectra obtained, thereby impacting the accuracy and effectiveness of the subsequent classification results.

BioFire® Joint Infection Panel for Samples Other than Synovial Fluid

Objectives: The early identification of infection-causing microorganisms through multiplex PCR panels enables prompt and targeted antibiotic therapy. This study aimed to assess the performance of the BioFire® Joint Infection Panel (BF-JIP) in analysing non-synovial fluid samples. Methods: We conducted a retrospective cohort study at Trieste University Hospital, Italy, on hospitalised adults with non-synovial fluid samples tested by both BF-JIP and traditional culture methods (November 2022–April 2024). Results: We evaluated 48 samples from 45 patients, including 24 abscess drainage fluids and 10 tissue samples. The BF-JIP showed high concordance (85.4%) and enhanced detection (4.3%) compared to culture methods. The BF-JIP excelled in cerebrospinal fluid (CSF) (100% accuracy and concordance) and in abscess drainage fluid (accuracy: 95.8%; concordance: 91.7%) identification and maintained high performance rates in patients under antibiotics. Conclusions: These findings suggest that BF-JIP is a valuable tool for accurate pathogen detection in various clinical samples, offering the additional advantage of being a rapid method.

What Is the Accuracy of 16S PCR Followed by Sanger Sequencing or Next-generation Sequencing in Native Vertebral Osteomyelitis? A Systematic Review and Meta-analysis.

Identifying a microorganism in patients with native vertebral osteomyelitis presents diagnostic challenges. Microorganism identification through culture-based methods is constrained by prolonged processing times and sensitivity limitations. Despite the availability of molecular diagnostic techniques for identifying microorganisms in native vertebral osteomyelitis, there is considerable variability in reported sensitivity and specificity across studies, leading to uncertainty in their clinical utility. What are the sensitivity, specificity, and diagnostic odds ratios for 16S broad-range PCR followed by Sanger sequencing (16S) and metagenomic next-generation sequencing (NGS) for detecting bacteria in native vertebral osteomyelitis? On June 29, 2023, we searched Cochrane, Embase, Medline, and Scopus for results from January 1970 to June 2023. Included studies involved adult patients with suspected native vertebral osteomyelitis undergoing molecular diagnostics-16S bacterial broad-range PCR followed by Sanger sequencing and shotgun or targeted metagenomic NGS-for bacteria detection. Studies involving nonnative vertebral osteomyelitis and cases of brucellar, tubercular, or fungal etiology were excluded. The reference standard for the diagnosis of native vertebral osteomyelitis was a composite clinical- and investigator-defined native vertebral osteomyelitis diagnosis. Diagnostic performance was assessed using a bivariate random-effects model. Risk of bias and diagnostic applicability were evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. After a manual screening of 3403 studies, 10 studies (5 on 16S, 5 on NGS) were included in the present analysis, from which 391 patients were included from a total of 958 patients overall. Quality assessment via QUADAS-2 criteria showed moderate risk of bias and good applicability. 16S showed 78% (95% confidence interval [CI] 95% CI 31% to 96%) sensitivity and 94% (95% CI 73% to 99%) specificity, whereas NGS demonstrated 82% (95% CI 63% to 93%) sensitivity and 71% (95% CI 37% to 91%) specificity. In addition, the diagnostic ORs were 59 (95% CI 9 to 388) and 11 (95% CI 4 to 35) for 16S and NGS, respectively. Summary receiver operating characteristic curves showed high test performance for 16S (area under the curve for 16S 95% [95% CI 93% to 97%] and for NGS 89% [95% CI 86% to 92%]). Certainty in estimates was moderate because of sample size limitations. This meta-analysis found moderate-to-high diagnostic performance of molecular methods on direct patient specimens for the diagnosis of native vertebral osteomyelitis. When used as a complementary test to microbiological analyses, a positive 16S result rules in the diagnosis of native vertebral osteomyelitis, while further studies are needed to understand the role of NGS in the diagnosis of native vertebral osteomyelitis. When available, these tests should be used in addition to conventional microbiology, especially in complex cases with extensively negative standard microbiological test results, to detect fastidious bacteria or to confirm the causative bacteria when their isolation and pathogenicity are unclear. A large sample size is needed in future research to understand the use of these techniques as standalone tests for diagnosis. Level III, diagnostic study.

Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes

BackgroundDeadwood decomposition is an essential ecological process in forest ecosystems, playing a key role in nutrient cycling and carbon sequestration by enriching soils with organic matter. This process is driven by diverse microbial communities encompassing specialized functions in breaking down organic matter, but the specific roles of individual microorganisms in this process are still not fully understood.ResultsHere, we characterized the deadwood microbiome in a natural mixed temperate forest in Central Europe using PacBio HiFi long-read sequencing and a genome-resolved transcriptomics approach in order to uncover key microbial contributors to wood decomposition. We obtained high quality assemblies, which allowed attribution of complex microbial functions such as nitrogen fixation to individual microbial taxa and enabled the recovery of metagenome-assembled genomes (MAGs) from both abundant and rare deadwood bacteria. We successfully assembled 69 MAGs (including 14 high-quality and 7 single-contig genomes) from 4 samples, representing most of the abundant bacterial phyla in deadwood. The MAGs exhibited a rich diversity of carbohydrate-active enzymes (CAZymes), with Myxococcota encoding the highest number of CAZymes and the full complement of enzymes required for cellulose decomposition. For the first time we observed active nitrogen fixation by Steroidobacteraceae, as well as hemicellulose degradation and chitin recycling by Patescibacteria. Furthermore, PacBio HiFi sequencing identified over 1000 biosynthetic gene clusters, highlighting a vast potential for secondary metabolite production in deadwood, particularly in Pseudomonadota and Myxococcota.ConclusionsPacBio HiFi long-read sequencing offers comprehensive insights into deadwood decomposition processes by advancing the identification of functional features involving multiple genes. It represents a robust tool for unraveling novel microbial genomes in complex ecosystems and allows the identification of key microorganisms contributing to deadwood decomposition.

Isolation and identification of endophytic microorganisms from orchids

Isolation and identification of endophytic microorganisms from orchids

Comparison of two automated urine cytometry systems: Sysmex® UF-1000i and Beckman Coulter® DxU 850 Iris

Background: Urinary tract infection, defined as the presence of bacteria or yeast in the urinary tract, is the most common community-acquired infection after respiratory infections. The cytobacteriological examination of urine (CBEU) remains the primary diagnostic test for urinary tract infections and is the most frequently conducted test in microbiology laboratories. Direct examination is a crucial step of CBEU, enabling the assessment of cytology, including leukocytes and red blood cells, as well as the identification of crystals, epithelial cells, and microorganisms when present in significant quantities. This examination also provides preliminary results that can guide clinical decision-making. While the standard method for urine cytology is a microscopic examination, automation offers several advantages, including standardized results with higher repeatability, improved reproducibility, increased sample throughput, and seamless data transfer to laboratory information systems. Objectives: This study aimed to compare the performance of two automated urine cytology systems: Sysmex UF-1000i and the Beckman Coulter DxU 850 Iris. Methods: We described the methodology and technology underlying each system and assessed their analytical performance. The UF-1000i uses flow cytometry for the objective characterization and identification of particles based on forward scattering, fluorescence, and adaptive typing analysis. In contrast, the DxU-850 Iris, a urine microscopy analyzer, employs proprietary digital flow morphology technology alongside automatic particle recognition software to isolate, identify, and characterize digital images of particles. Conclusion: Our comparison showed that both systems performed exceptionally well, delivering results that are comparable, and, in some cases, superior to, those obtained through the reference method of optical microscopy.

Molecular design strategy for microorganism discrimination based on keto-salicylaldehyde azine derivatives

The rapid and selective identification of microorganisms is of great significance for clinical therapy applications. To develop high performance probes for microbe determination, we systemically constructed series aggregation-induced emission (AIE) luminogens by modulating the structural planarity, the basicity of functional group, the length of linker moiety and the hydrophobicity based on our previous work. The detail structure-property relationship study based on experimental and theoretical observation revealed that: i) the planar skeleton is essential for probe insertion towards the cell wall via van n der Waals' force. ii) the basic function group enable the anchoring on the membrane by binding with acidic biomolecules. iii) the shortened alkyl chain is in favor of the efficient binding of basic groups with microbes and endows the desirable hydrophobicity. Based on the developed probes, the successful detection of the pathogens in clinic samples was achieved in highly sensitive and simple way. This work provides a reliable strategy for designing intelligent luminogens for microorganism discrimination and identification in efficient and sensitive way for in vitro diagnosis applications, especially point-of-care testing (POCT).

Lactobacillus reuteri metabolites alleviate apple replant disease (ARD) by driving beneficial bacteria to reshape the core root microbiome

Previous studies have shown that the bacterial fertilizer Lactobacillus reuteri (LBR) significantly alleviates apple replant disease (ARD), but the mechanism behind its effectiveness remains unclear. This study investigated the effects of key LBR metabolites on the rhizosphere microbial community. The biocontrol function of extracellular polysaccharides (EPS) was examined and shown to be further enhanced after optimizing the fermentation conditions. The optimized fermentation conditions were found to generate intermediates involved in various plant metabolic pathways, leading to plant growth promotion, increased abundance of beneficial bacteria like Bacillus and Pseudomonas in the rhizosphere soil, and decreased abundance of pathogenic fungi. Through the isolation and identification of rhizosphere microorganisms, a strain of Pseudomonas monteilii with chemotaxis to EPS was isolated, which had growth promotion ability and effectively improved plant resistance and relieves ARD. To further understand the mechanism underlying the inhibitory effect on soil pathogens of microbial aggregations and development in the rhizosphere driven by beneficial bacteria metabolites. These findings offer valuable technical insights for utilizing biocontrol bacteria metabolites in ARD management.

The Effects of Predominantly Chemoautotrophic Versus Heterotrophic Biofloc Systems on Nitrifying Bacteria, Planktonic Microorganisms, and Growth of Penaeus vannamei, and Oreochromis niloticus in an Integrated Multitrophic Culture

The aim of this study was to evaluate the effect of predominantly chemoautotrophic and heterotrophic biofloc systems on ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), and planktonic microorganisms in an integrated Penaeus vannamei and Oreochromis niloticus integrated multitrophic culture. Shrimp and tilapia were stocked at a density of 400 shrimp m−2 and 45 fish m−3, respectively. The trial consisted of two biofloc treatments, with three replicates each: chemoautotrophic and heterotrophic. The identification and quantification of the planktonic microorganisms (ciliates, flagellates, microalgae, and total bacteria) and nitrifying bacteria were carried out through direct counting and fluorescence in situ hybridization, respectively. At the end of the trial, heterotrophic treatment had resulted in higher total abundance of bacteria. The relative abundance of AOB and NOB in relation to the total abundance was less than 0.1% for both treatments. The system was dominated by flagellates in both treatment groups. The abundance of microalgae and ciliates was higher with chemoautotrophic treatment. After 43 days, the shrimp weights were higher in the chemoautotrophic group, while the final weights of the tilapia were not significantly different between the two treatments. The type of biofloc system (Chemoautotrophic vs. Heterotrophic) did not significantly alter the establishment of AOB and NOB in a Penaeus vannamei and Oreochromis niloticus integrated multitrophic culture. The two treatments proved to be equally efficient for maintaining good water quality, but the chemoautotrophic treatment resulted in better shrimp growth. Thus, our study demonstrated that chemoautotrophic biofloc is a promising approach in integrated multitrophic aquaculture.

THE ETIOLOGICAL PROFILE AND ALTERATIONS IN CEREBROSPINAL FLUID CHARACTERISTICS IN PATIENTS WITH BACTERIAL MENINGITIS

Currently, bacterial meningitis (BM) remains a form of life-threatening infectious pathology, with a mortality rate ranging from 4% to 35% and poor prognosis often accompanied by diverse specific and non-specific complications, including infectious toxic shock, cerebral edema, ventricular inflammation, hydrocephalus, acute cerebrovascular accidents, venous sinus thrombosis, disseminated intravascular coagulation (DIC) syndrome, respiratory distress syndrome (RDS) syndrome, inappropriate secretion of antidiuretic hormone, and systemic inflammatory response syndrome. In clinical practice, the early identification of the causative microorganism and the implementation of proper antibiotic treatment, as well as a comprehensive assessment of the patient's status and management, are crucial for minimizing a risk of related severe complications and mortality. The BM etiology is characterized by a highly variable nature, contingent upon a multitude of factors such as geographic location, temporal context, patient age, immunological status, and other variables. Over the past two to three decades, advancements in conjugate vaccines and the use implementation of antibiotic treatment have brought about alterations in the spectrum of pathogens responsible for meningitis. The objective of this study was to delve into the etiological profile and prognostic implications of cerebrospinal fluid (CSF) parameters among patients with diagnosed meningitis admitted to the Neuroinfectious Diseases Division of the Infectious Clinical Hospital №2 (Moscow) between 2022 and 2023. A retrospective analysis of medical records of meningitis patients admitted to the Infectious Clinical Hospital №2 during 2022–2023 was conducted. The data were analyzed using the k-means clustering algorithm implemented in the Loginom analytics software to create a scenario, as well as OLAP cubes. The study involved the analysis of medical records for 110 patients aged 18-89 years old. Among the BM pathogens identified, Neisseria meningitidis emerged as the most prevalent in this patient cohort, accounting for 68.2% of cases. Within the group of meningococcal meningitis cases, serovariants A and W135 were the most frequently detected, accounting for 49.3% and 33.3%, respectively. Significant alterations in cerebrospinal fluid parameters, characterized by elevated cell counts and lowered glucose levels, were observed among patients with purulent meningitis resulting from serogroup A Neisseria meningitidis infections. A combination of elevated baseline cell level along with high concentrations of proteins, and lactate, coupled with the presence of D-dimer in cerebrospinal fluid, has been associated with a severe disease progression and the emergence of critical and life-threatening sequelae.

Study Effect of Peppermint Extract on Microorganisms Isolation and Identification from Pizza

Study Effect of Peppermint Extract on Microorganisms Isolation and Identification from Pizza

IDENTIFICATION AND SUSCEPTIBILITY TO ANTIBIOTICS OF BACTERIA ISOLATED FROM MASTITIS MILK FROM THE NORTHERN MESOREGION OF THE STATE OF RIO DE JANEIRO

Milk production is one of the main activities of Brazilian livestock farming. Among the diseases that cause the greatest economic losses to producers, mastitis is the most recurrent. 805 cows were tested using the “California Mastitis Test” (CMT) on 54 farms in the northern mesoregion of the State of Rio de Janeiro. 45.96% (370) tested positive for subclinical mastitis. Milk samples were then collected and subjected to culture and identification of microorganisms according to routine laboratory tests, and an antibiogram was performed shortly thereafter. In 28.4% (105) of the samples, Staphylococcus aureus was identified, followed by 25.1% (93) Streptococcus spp., 10.8% (40) Streptococcus agalactiae, Staphylococcus spp., 8.4% (31), 7.8% (29) Corynebacterium bovis, 0.8% (3) Streptococcus sanguis, 23.2% (86) of the plates with culture medium showed no growth. The antibiogram of 105 strains of Staphylococcus aureus, 83.8% (88) demonstrated resistance to penicillin, it was also observed that 24.7% (26) were resistant to tetracycline. Of the 40 strains of Streptococcus agalactiae, 57.5% (23) were resistant to tetracycline, 18 (45%) were resistant to enrofloxacin and 11 (27.5%) were resistant to gentamicin. The bacteria Staphylococcus aureus, Staphylococcus spp. and Streptococcus agalactiae were the most isolated and showed resistance to antibiotics. These results are of concern for both animal and human health, since Staphylococcus aureus in particular can infect humans.

Exploring microbial diversity and functionality in Verdejo wine vinegar fermentation through LC-MS/MS analysis

The identification of microorganisms in vinegar production remains a challenge mainly, due to the difficulty of isolating and characterizing the microbiota involved. This implies that despite progress in understanding the composition and role of these microbial communities, there are still virtually unknown microorganisms in these environments. Metaproteomics reveals microbial diversity and behavior by analysis of proteins, offering precise insights into key moments and conditions in biological processes like acetification. This study consists of a thorough metaproteomic analysis during the elaboration of an innovative vinegar, Verdejo wine vinegar. Acetic acid fermentation occurred by submerged culture in an 8L automated Frings reactor operated in semi-continuous mode. LC-MS/MS identified 1626 proteins from 149 taxonomic groups, mainly Acetobacteraceae (1529), followed by yeast (47), lactic acid bacteria (29), and Archaea (21). Komagataeibacter (73.7%), Acetobacter (10.7%), Gluconacetobacter (1.7%), Novacetimonas (1.6%), and Gluconobacter (1.3%) were prevalent genera, with K. europaeus being the dominant species (56.7%). To our knowledge, this is the first metaproteomic approach to comprehensively address the study of so diverse microbial populations. GO Term analysis emphasized "heterocyclic compound binding" and "organic substance metabolic process", while analysis of protein-protein interactions identified key metabolic processes, such as amino acid biosynthesis, especially BCAAs, and crucial energetic pathways such as the TCA cycle. Stress response mechanisms, such as the dnaK-dnaJ-grpE and cl2p system, have been also highlighted. These analyses revealed the molecular and functional complexity of the acetification process, highlighting the critical importance of diverse metabolic routes in the adaptation of the microbiota members to the medium conditions. Overall, this study aims to characterize the microbiota driving Verdejo wine acetification and explore its composition, functions, and key metabolic processes.

Machine Learning Approaches for Microorganism Identification, Virulence Assessment, and Antimicrobial Susceptibility Evaluation Using DNA Sequencing Methods: A Systematic Review.

Microbial infections pose a substantial global health challenge, particularly impacting immunocompromised individuals and exacerbating the issue of antimicrobial resistance (AMR). High virulence of pathogens can lead to severe infections and prolonged antimicrobial treatment, increasing the risk of developing resistant strains. Integrating machine-learning (ML) with DNA sequencing technologies offers potential solutions by enhancing microbial identification, virulence assessment, and antimicrobial susceptibility evaluation. This review explores recent advancements in these integrated approaches, addressing current limitations and identifying gaps in the literature. A comprehensive literature search was conducted across databases including PubMed, Scopus, Web of Science, and IEEE Xplore, covering publications from January 2014 to June 2024. Using a detailed Boolean search string, relevant studies focusing on ML applications in microorganism identification, antimicrobial susceptibility testing, and microbial virulence were included. The screening process involved a two-stage review of titles, abstracts, and full texts, with data extraction and critical appraisal performed using the QIAO tool. Data were analyzed through narrative synthesis to identify common themes and innovations. Out of 1,650 initially identified records, 19 studies met the inclusion criteria. These studies primarily focused on AMR, with additional research on microbial virulence and identification. Machine learning algorithms such as Random Forest, Support Vector Machines, and Convolutional Neural Networks, combined with DNA sequencing techniques like Whole Genome Sequencing and Metagenomic Sequencing, demonstrated significant advancements in predictive accuracy and efficiency. High-quality studies achieved impressive performance metrics, including F1-scores up to 0.88 and AUC scores up to 0.96. The integration of ML and DNA sequencing technologies has significantly enhanced microbial analysis, improving the identification of pathogens, assessment of virulence, and evaluation of antimicrobial susceptibility. Despite advancements, challenges such as data quality, high costs, and model interpretability persist. This review highlights the need for continued innovation and provides recommendations for future research to address these limitations and improve disease management and public health strategies. The systematic review is registered with PROSPERO (CRD42024571347).

Exploring the value of hybrid capture-based next-generation sequencing technology in the suspected diagnosis of bloodstream infections.

Determining the source of infection is significant for the treatment of bloodstream infections (BSI). The gold standard of blood infection detection, blood cultures, have low positive rates to meet clinical needs. In this study, we investigated the ability of hybrid capture-based next generation sequencing technology to detect pathogens in peripheral blood samples collected from patients with suspected BSI. Blood cultures and capture sequencing assays were also analyzed against the final clinical diagnoses. In this study, peripheral blood samples were collected from patients with fever, chills, and suspected BSI at Jinshazhou Hospital of Guangzhou University of Chinese Medicine from March 2023 to January 2024. All samples were tested by three different technologies: plasma capture sequencing technology, white blood cell capture sequencing technology, and blood culture. Relevant clinical diagnostic information was also collected. The performances of the blood cultures were then compared to those of both plasma capture sequencing technology and white blood cell capture sequencing technology. A total of 98 patients were included in this study. The positive rates of probe capture next generation sequencing (NGS technology) in plasma and white blood cells were 81.63% and 65.31%, respectively, which were both significantly higher than that of the blood culture, which was 21.43% (p <0.001). Taking blood culture as the standard control, the sensitivity and specificity of plasma capture sequencing were 85.71% and 71.43%, respectively, while the sensitivity and specificity of white blood cell sequencing were 76.19% and 81.82%, respectively. Upon final clinical diagnosis, the clinical agreement rates of the blood cultures, plasma capture sequencing, and white blood cell capture sequencing were 39.80%, 83.67%, and 73.47%, respectively. Our study demonstrates the high accuracy of probe capture sequencing technology compared to blood cultures in the identification of pathogenic microorganisms in BSI upon final clinical diagnosis. Among the different sample types, white blood cell samples had a lower clinical compliance rate compared to plasma samples, possibly due to the higher host rate in cell samples, which impairs the sensitivity of pathogen detection.

Identification of causative and non-causative microorganisms of nephrostomy tube-associated pyelonephritis among patients with malignancy

BackgroundProlonged installation of a nephrostomy tube causes colonization of various microorganisms within the lumen of the tube, leading to the development of nephrostomy tube-associated pyelonephritis (NTAP). Patients with malignancy, often necessitating long-term installation of a nephrostomy tube, are susceptible to NTAP. However, information regarding the characteristics of NTAP in this population is limited. MethodsWe reviewed 43 NTAP cases of patients with malignancy in a cancer center and examined causative and non-causative microorganisms among those detected in urine culture. Causative microorganisms were defined as (1) those detected simultaneously in urine and blood cultures or (2) those detected in monomicrobial urine culture and to which physicians administered active antimicrobials for ≥5 days. Non-causative microorganisms were defined as those to which active antimicrobials were given for a total of <5 days. ResultsPatients in 42 of the 43 NTAP cases recovered with antimicrobial therapy for ≥7 days. Causative microorganisms were identified in 25 cases, where Escherichia coli and Klebsiella pneumoniae were most frequent. All enterococci other than Enterococcus faecalis, Corynebacterium species, and Candida species other than Candida albicans and most of Stenotrophomonas maltophilia detected in urine culture were considered non-causative of NTAP. ConclusionE. coli was a common organism causing NTAP of this population. Several microorganisms resistant to cephalosporin were non-causative of NTAP, for which administration of antimicrobials may be unnecessary even if detected in urine culture.

Accuracy of various matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based rapid identification methods—As a tool to augment diagnostic stewardship in blood culture laboratory, South India

BackgroundBlood stream infection is a medical emergency associated with high morbidity and mortality. Prompt identification of bloodstream infection-causing microorganisms directly from positive blood culture will significantly enhance patient care by reducing the turnaround time of pathogen recognition. MethodsA total of 256 freshly flagged positive blood culture bottles were subjected to Gram staining. Direct MALDI-TOF MS analysis was performed following sample preparation techniques such as lysis centrifugation, lysis filtration and VITEK® MS BC kit to directly identify microorganisms from positive blood cultures. Along with these short-term incubation methods of Choco spot and minute colony(8–10h) were also performed. All those positive bottles were identified by the routine (reference) laboratory method. Results177 isolates (69.14 %) were correctly identified by Lysis centrifugation, 163 isolates (63.67 %) were correctly identified by Lysis filtration, 206 isolates (80.47 %) were correctly identified by Choco spot,250 isolates (97.65 %) were correctly identified from minute colony (8–10h) of incubation. Of 162 isolates,115 isolates (70.99 %) were correctly identified by VITEK® MS Blood culture kit, (BioMérieux). VITEK® MS BC kit method revealed higher agreement with the kappa value of 0.697 than lysis centrifugation (0.672) followed by lysis filtration (0.611). ConclusionsIn house method of lysis centrifugation is found to be equivalent to VITEK® MS BC kit method and superior to lysis filtration method in correct direct identification of bacteria from positive blood cultures by MALDI-TOF MS analysis. As lysis centrifugation requires only 10 min of processing time as compared to overnight incubation, thus it offers a less expensive substitute for the VITEK® MS BC kit in the clinical laboratory. As a consequence of this study, we have implemented direct MALDI-TOF-based identification from positive BCs in our daily routine diagnostic management.

Influence of soil microplastic contamination on maize (Zea mays) development and microbial dynamics

BackgroundMicroplastics are contaminants in soil ecosystems that alter biophysical processes, affect plant growth, ecosystems and humans in the long run. This study was conducted to investigate the influence of soil microplastic contamination on the growth, development, and microbial dynamics of maize (Zea mays).Composite soil samples were collected from the farm from 0 to 10 cm depth. Physicochemical properties were assessed before maize seed sowing. Three soil weight categories were treated with 30 g, 20 g and 10 g microplastics. Soil physicochemical properties and heavy metal content in maize plants were analyzed. Morphological parameters, microbial counts, and microorganism identification were conducted. FTIR analysis was carried out in selected plant parts.ResultsThe study revealed a pH range of 5.00–6.70, electrical conductivity of 70–158 µS/cm, organic carbon and organic matter, total nitrogen, average phosphorus content, clay and silt content. The concentrations of heavy metals in plant parts were within WHO standard limits of 425.5 and 500 mg/kg for iron and manganese, but above the limits of 40, 60, and 350 mg/kg for copper, zinc and magnesium. The plant had various leaf sizes and heights, with chlorosis and necrotic activity ranging from 0.33 to 2.67, and a range of 1.33 to 6.33, respectively. Soil samples showed a total bacterial count (TBC) of 2.00 × 103 cfu/g to 7.60 × 104 cfu/g and a total fungal count (TFC) of 4.00 × 103 cfu/g to 2.20 × 104 cfu/g. Pseudomonas aeruginosa, Bacillus subtilis, Escherichia coli, Staphylococcus epidermidis, Proteus mirabilis and Bacillus cereus had percentage occurrences of 44.31, 21.17, 9.12, and 3.26%, respectively. Penicillium notatum was the most prevalent, while Fusarium spp. was the least prevalent. The FTIR analysis of maize seeds from soil samples A, B, and C revealed various organic compounds, with opium powder and streptomycin sulphate being the most abundant. The study revealed that pot B had the highest microplastic concentration at 1 WAS, while pot C had the lowest at 0.10 mg/kg, indicating a differential soil microplastic accumulation.ConclusionMicroplastics impact soil health, plant growth, and nutrient cycling, necessitating sustainable agriculture. Long-term research is needed to understand ecological and physiological impacts and explore remediation techniques.

Effective technology of disinfecting ozonation of hatching chicken eggs

Relevance. The positive aspects of disinfecting ozonation of hatching eggs allow us to expect successful application of the method not only in large but also in small-scale farms, as well as for experimental and industrial purposes in laboratories and bio-enterprises related to the technological process based on the incubation of a small number of eggs. This determines the importance of expanding the range of ozonizers due to numerous portable devices. There are no clear recommendations for these devices and this causes the need to search for the most effective and harmless modes for the embryo, and schemes of disinfecting ozonation.Methods. The study used fertilized chicken eggs “Hysex Brown” and a portable ozonizer “OZON-OviV”. Ozone concentration 2.0 mg / l. Eggs were treated in a specially made chamber. Technology-1: twice for 30 minutes before incubation and on the 3rd day of incubation. Technology-2: three times for 30 minutes before incubation, on days 3 and 5. The range of studies included: assessment of total microbial contamination (densitometry); identification of microorganisms (MALDI-TOF-spectrometry); biological control of incubation (fertility, hatchability, mortality, developmental abnormalities); assessment of the adequacy of the internal organs (MicroCT); embryo morphometry (weight, length, chest circumference) and calculation of development proportionality indices; histological assessment of the liver.Results. The total ozone concentration during treatment by two methods was 240 mg/l and 360 mg/l, respectively. The disinfecting efficiency of ozonation has been proven, providing a decrease in the level of total microbial contamination by 30% and 40% with double and triple treatment. A tendency to maintain a low total microbial contamination, compared to intact eggs, up to 14 days of incubation has been revealed. The dynamics of the microbial landscape indicate the bacteriostatic effect of ozone in the concentrations used on a wide range of microorganisms. Microtomographic and histological methods confirmed the harmlessness of the technologies used. Along with the more pronounced antibacterial effect of technology-2, the presence of a stimulating effect on the body of the developing embryo was revealed, which determines the preference for its choice.

Can bone SPECT/CT determine optimal sites for microbiological identification in post-traumatic or chronic osteomyelitis of extremities?

IntroductionAccurate microbiological identification is crucial when managing chronic osteomyelitis (COM) and post-traumatic osteomyelitis (PTO). Although bone single photon emission computed tomography/computed tomography (SPECT/CT) has helped in localizing osteomyelitis lesions, its effectiveness in guiding microbiological sampling remains unclear. This study aimed to determine whether bone SPECT/CT can improve microbiological identification rates in COM or PTO of the extremities. Patients and methodsFrom February 2020 to August 2024, 53 patients with suspected COM or PTO in the extremities were retrospectively analyzed. All patients underwent bone SPECT/CT, followed by microbiological sampling during surgery. Tissue samples were taken from the areas of high SPECT/CT uptake or based on intraoperative findings where no uptake was observed. Microorganism identification rates were analyzed, including a sub-group analysis based on antibiotic discontinuation. ResultsOf the 53 patients, 42 had positive bone SPECT/CT scan findings, with pathogen identification in 30 patients (71.4 %). In contrast, pathogen identification occurred in one out of twelve patients (9.1 %) with negative findings (odds ratio 25, p< 0.001). Bone SPECT/CT demonstrated a sensitivity of 96.8 % and an overall accuracy of 75.5 %. When antibiotics had been discontinued for ≥2 weeks, the pathogen identification rate increased to 90 %, compared with 50 % for <2 weeks of discontinuation (odds ratio 10.0, p= 0.006). In a sub-group of 30 patients with adequate antibiotic discontinuation duration, a positive bone SPECT/CT scan yielded a pathogen identification rate of 90.1 % (odds ratio 60.0, p= 0.001). ConclusionBone SPECT/CT effectively identifies optimal sites for microbiological sampling in COM and PTO of the extremities, particularly when antibiotics have been discontinued for ≥2 weeks, enhancing pathogen detection rates.