Identification Of Bacterial Species Research Articles

Evaluating the Genome-Based Average Nucleotide Identity Calculation for Identification of Twelve Yeast Species.

Classifying a yeast strain into a recognized species is not always straightforward. Currently, the taxonomic delineation of yeast strains involves multiple approaches covering phenotypic characteristics and molecular methodologies, including genome-based analysis. The aim of this study was to evaluate the suitability of the Average Nucleotide Identity (ANI) calculation through FastANI, a tool created for bacterial species identification, for the assignment of strains to some yeast species. FastANI, the alignment of in silico-extracted D1/D2 sequences of LSU rRNA, and multiple alignments of orthologous genes (MAOG) were employed to analyze 644 assemblies from 12 yeast genera, encompassing various species, and on a dataset of hybrid Saccharomyces species. Overall, the analysis showed high consistency between results obtained with FastANI and MAOG, although, FastANI proved to be more discriminating than the other two methods applied to genomic sequences. In particular, FastANI was effective in distinguishing between strains belonging to different species, defining clear boundaries between them (cutoff: 94-96%). Our results show that FastANI is a reliable method for attributing a known yeast species to a particular strain. Moreover, although hybridization events make species discrimination more complex, it was revealed to be useful in the identification of these cases. We suggest its inclusion as a key component in a comprehensive approach to species delineation. Using this approach with a larger number of yeasts would validate it as a rapid technique to identify yeasts based on whole genome sequences.

Differential Sensing Approach as a Pattern-based Discrimination for Biological Samples.

The differential sensing approach uses fingerprint patterning to distinguish uncharacterized biological samples. Inspired by natural sensory systems, an array of cross-reactive sensors generates unique response fingerprint depending on the samples. Until today, this array system has been developed using various materials, including the library of surface-charged nanoparticles and chemosensors. Many differential array systems have demonstrated accurate identification of bacterial species, viral subtypes, and cancer cells, as well as distinguishing disease states in blood or urine. This capability is particularly important for distinguishing between normal and abnormal states when specific marker molecules have not yet been identified, providing a powerful diagnostic tool. In this concept, we summarized representative outcomes of differential sensing applications for biological sample discrimination.

Nanoplasmonic Rapid Antimicrobial-Resistance Point-of-Care Identification Device: RAPIDx.

The emergence of antibiotic resistance has become a global health crisis, and everyone must arm themselves with wisdom to effectively combat the "silent tsunami" of infections that are no longer treatable with antibiotics. However, the overuse or inappropriate use of unnecessary antibiotics is still routine for administering them due to the unavailability of rapid, precise, and point-of-care assays. Here, a rapid antimicrobial-resistance point-of-care identification device (RAPIDx) is reported for the accurate and simultaneous identification of bacterial species (genotype) and target enzyme activity (phenotype). First, a contamination-free active target enzyme is extracted via the photothermal lysis of preconcentrated bacteria cells on a nanoplasmonic functional layer on-chip. Second, the rapid, precise identification of pathogens is achieved by the photonic rolling circle amplification of DNA on a chip. Third, the simultaneous identification of bacterial species (genotype) and target enzyme activity (phenotype) is demonstrated within a sample-to-answer 45min operation via the RAPIDx. It is believed that the RAPIDx will be a valuable method for solving the bottleneck of employing on-chip nanotechnology for antibiotic-resistant bioassay and other infectious diseases.

Towards unified reporting of genome sequencing results in clinical microbiology.

Whole genome sequencing (WGS) has become a vital tool in clinical microbiology, playing an important role in outbreak investigations, molecular surveillance, and identification of bacterial species, resistance mechanisms and virulence factors. However, the complexity of WGS data presents challenges in interpretation and reporting, requiring tailored strategies to enhance efficiency and impact. This study explores the diverse needs of key stakeholders in healthcare, including clinical management, laboratory work, public surveillance and epidemiology, infection prevention and control, and academic research, regarding WGS-based reporting of clinically relevant bacterial species. In order to determine preferences regarding WGS reports, human-centered design approach was employed, involving an online survey and a subsequent workshop with stakeholders. The survey gathered responses from 64 participants representing the above mentioned healthcare sectors across geographical regions. Key findings include the identification of barriers related to data accessibility, integration with patient records, and the complexity of interpreting WGS results. As the participants designed their ideal report using nine pre-defined sections of a typical WGS report, differences in needs regarding report structure and content across stakeholders became evident. The workshop discussions further highlighted the need to feature critical findings and quality metrics prominently in reports, as well as the demand for flexible report designs. Commonalities were observed across stakeholder-specific reporting templates, such as the uniform ranking of certain report sections, but preferences regarding the depth of content within these sections varied. Using these findings, we suggest stakeholder-specific structures which should be considered when designing customized reporting templates. In conclusion, this study underscores the importance of tailoring WGS-based reports of clinically relevant bacteria to meet the distinct needs of diverse healthcare stakeholders. The evolving landscape of digital reporting increases the opportunities with respect to WGS reporting and its utility in managing infectious diseases and public health surveillance.

Inhibition Rates of Disinfectants on Bacterial Isolated from Student Dormitory

Background: Although most of human life is spent inside, where bacteria are always present on things, little is known about the microbial variety of indoor habitats. Objectives: The major objective of this study was to determine the rate and types of bacterial contaminants in female and male student dormitory of Al-Kufa university campus, and to explore the inhibitory effect of certain disinfectants. This study was conducted for the period from October 2022 to Jun 2023. A total of 400 bacteriological swabs were collected aseptically from different sites of male and female student dormitory of Al-Kufa university. Swabs were streaked as soon as possible on blood agar and MaConkey agar plates and incubated overnight. Identification of bacterial species was based on standard bacteriological criteria. The inhibitory effect of 40% and 60% concentrations of three commercially available disinfectants; dettol (chloroxylenol), Al-Emlaq (Alkyl benzene sulfonate), and the house bleach (sodium hypochlorite) were explored by agar diffusion method. Data were statistically analyzed. Results: The results revealed that the overall bacterial contamination rate in student’s dormitories of Al-Kufa university campus was 78%. Male dormitory unit had significantly higher contamination rate compared to female dormitory unit (57.5% vs 42.5%). Bacillus spp. Was the most predominant contaminant in both male and female units. Al-Emlaq super gel (Alkyl benzene sulfonate) was found as the most effective disinfectant against the majority of bacterial isolates. Conclusion: Authorized and public awareness toward bacterial contamination in student's dormitories is recommended. The selection of an effective disinfectant should be based on its active ingredient and concentration.

Antibacterial Effect of Silver Nanoparticles against Oral Biofilms in Subjects with Motor and Intellectual Disabilities.

Motor and intellectual disabilities (MIDs) represent a great challenge for maintaining general health due to physical and cognitive limitations, particularly in the maintenance and preservation of oral health. Silver nanoparticles (AgNPs) have emerged as a promising therapeutic tool for bacterial control, including oral biofilms; however, knowledge of the bactericidal effectiveness of oral biofilms from patients with MIDs is insufficient. This study aims to determine the antimicrobial effect of AgNPs on different oral biofilms taken from patients with and without MIDs. Two sizes of AgNPs were prepared and characterized by dynamic light scattering (DLS) and transmission electron microscopy (TEM). Through consecutive sampling, biofilm samples were collected from 17 subjects with MIDs and 20 subjects without disorders. The antimicrobial effect was determined by obtaining the minimum inhibitory concentration (MIC) of AgNPs, and the identification and distribution of oral bacterial species were determined by polymerase chain reaction (PCR). Finally, correlations between sociodemographic characteristics and the antimicrobial levels of AgNPs were also explored. The values of the MIC results were analyzed with IBM-SPSS software (version25) using non-parametric tests for independent groups and correlations, with statistical significance being considered as p < 0.05. Both sizes of AgNPs exhibited tight particle size distributions (smaller: 10.2 ± 0.7 nm; larger: 29.3 ± 2.3 nm) with zeta potential values (-35.0 ± 3.3 and -52.6 ± 8.5 mV, respectively) confirming the stability that resulted in little to no agglomeration of nanoparticles. Although both sizes of AgNPs had good antimicrobial activity in all oral biofilms, the smallest particles had the best antimicrobial effects on the oral biofilm samples from patients with and without MIDs, even better than chlorhexidine (CHX) (p < 0.05). Likewise, the patients with disabilities showed higher levels of antimicrobial sensitivity to AgNPs compared with CHX (p < 0.05). Although the microorganisms included in the biofilms of females had a statistically higher growth level, the AgNP antimicrobial effect was statistically similar in both genders (p > 0.05). The most frequent bacteria for all oral biofilms were S. mutans (100%), P. intermedia (91.6%), T. forsythia (75.0%), T. denticola (75.0%), P. gingivalis (66.6%), F. nucleatum (66.6%), S. sobrinus (50.0%), and A. actinomycetemcomitans (8.3%). AgNPs exhibited considerable antimicrobial potential to be used as a complementary and alternative tool in maintaining and preserving oral health in patients with MIDs.

Protein Concentration, Anthelmintic Activity, and Microbial Contamination of the Laboratory-Produced Chitosan-Encapsulated Bromelain Batches

Bromelain has been shown to have potential as an anthelmintic for controlling livestock nematodes, such as Haemonchus (H.) contortus. The present study aimed to evaluate the in vitro quality of the laboratory-produced nanoencapsulated bromelain (NEB) and its activity against H. contortus. The acid-base extraction method was employed to extract four different batches of bromelain from the peels of fully ripened pineapples. It was encapsulated in chitosan to form the nano-encapsulated bromelain complex. Standard biochemical methods were employed to determine the bromelain concentration, protein concentration, in vitro anthelmintic activity against various stages of H. contortus (egg, larva, adult), and bacteria contamination for the four NEB batches. The mean concentration of extracted bromelain was 4.3 mg/ml in all four batches. There were no variations in the protein concentrations between the batches of NEB, which ranged from 1,090 mg/ml to 1.205 mg/ml. Although there were no significant differences in different batches, a variation in NEB inhibitory concentration (IC50) was observed according to the different parasitic stages. The highest activity was for adult worms (LC50 =0.2454 ± 0.05 mg/ml), followed by the eggs (IC50 = 0.3 ± 0.07 mg/ml), and the larval stage (IC50 =0.9 ± 0.45 mg/ml). Despite the identification of certain bacterial species in the raw pineapple extract, the final product of all four batches of NEB remained free from any bacterial contamination. The current study indicated that NEB's concentration, protein concentrations, and anthelmintic activity did not vary significantly across the different batches of NEB. Additionally, the encapsulation process ensured that the final product was free of bacterial contamination and thus safe for use in animals.

Identification of novel bacterial species in the blood of patients with neonatal sepsis

BackgroundThe clinical diagnosis of neonatal sepsis remains difficult because of various challenges, such as culturing the bacteria and avoiding contamination. Therefore, this study aimed to identify bacterial pathogens in patients with clinically diagnosed neonatal sepsis by next-generation sequencing (NGS).MethodsHigh-throughput NGS and traditional culture identification were performed by comparing samples from newborns with neonatal sepsis with healthy control infants. All blood samples were separately inoculated into anaerobic and aerobic bottles and incubated for 7 days at 37 °C, the positive specimens were then identified. Novel bacteria identified through high-throughput NGS were analysed using polymerase chain reaction (PCR), PCR products were verified by Sanger sequencing. Wilcoxon rank-sum and chi-square tests were performed to assess the significance of differences in species abundance between groups. Subjects were clinically diagnosed and hospitalized at the Pediatrics Department of Shenzhen Seventh People’s Hospital and Pediatrics Department of the Longhua Branch of Shenzhen People’s Hospital. Experiments were performed at the Shenzhen Seventh People’s Hospital. The experimental group comprised 45 newborns clinically diagnosed with neonatal sepsis (age: 0–28 days; 28 males, 17 females). Fifteen normal newborns aged 0–28 days (7 males, 8 females) were included as the control group.ResultsHigh-throughput NGS showed a positivity rate of 44% (20/45) for bacteria in patients clinically diagnosed with neonatal sepsis, whereas traditional bacterial culture identification showed a positivity rate of 0% (0/45). The four main bacterial species identified were Anoxybacillus kestanbolensis, Geobacillus vulcani, Klebsiella oxytoca, and Acinetobacter guillouiae.ConclusionsA. kestanbolensis, G. vulcani, K. oxytoca, and A. guillouiae, newly discovered bacteria in patients with neonatal sepsis, were identified with high-throughput NGS. Which may result from maternal intrauterine infection or birth-canal infection and have a high clinical-cure rate. Owing to a lack of methods to culture these bacteria, their role in neonatal sepsis remains unclear. A definite diagnosis cannot rely solely on bacterial culture identification for patients with a suspected diagnosis and clinical diagnosis of neonatal sepsis and should involve other effective diagnostic techniques.

Improved Classification Performance of Bacteria in Interference Using Raman and Fourier-Transform Infrared Spectroscopy Combined with Machine Learning.

The rapid and sensitive detection of pathogenic and suspicious bioaerosols are essential for public health protection. The impact of pollen on the identification of bacterial species by Raman and Fourier-Transform Infrared (FTIR) spectra cannot be overlooked. The spectral features of the fourteen class samples were preprocessed and extracted by machine learning algorithms to serve as input data for training purposes. The two types of spectral data were classified using classification models. The partial least squares discriminant analysis (PLS-DA) model achieved classification accuracies of 78.57% and 92.85%, respectively. The Raman spectral data were accurately classified by the support vector machine (SVM) algorithm, with a 100% accuracy rate. The two spectra and their fusion data were correctly classified with 100% accuracy by the random forest (RF) algorithm. The spectral processed algorithms investigated provide an efficient method for eliminating the impact of pollen interference.

Chromosomal and plasmid localization of ileS2 in high-level mupirocin-resistant Staphylococcus pseudintermedius and Staphylococcus aureus isolated from canine and feline origins.

To characterize the mobile genetic elements and genetic localization of ileS2 in high-level mupirocin-resistant (Hi-MupR) methicillin-resistant Staphylococcus pseudintermedius (MRSP) and MRSA isolates recovered from canine and feline clinical samples. The identification of bacterial species and presence of mecA and ileS2 genes in MRSP and MRSA isolates were performed using MALDI-TOF MS and PCR, respectively. Antimicrobial resistance (AMR) phenotypes were determined by broth microdilution assays. The genome characteristics, ileS2-containing elements and staphylococcal cassette chromosome mec (SCCmec) were illustrated using complete circular genomes obtained from hybrid assembly of Illumina short-reads and Oxford Nanopore Technologies long-reads. These were analysed through phylogenetic and bioinformatics approaches. A total of 18 MRSP clinical isolates and four MRSA clinical isolates exhibited the Hi-MupR phenotype and carried multiple AMR genes, including mecA and ileS2 genes. MRSP ST182-SCCmec V (n = 6) and ST282-ΨSCCmec57395-t10 (n = 4) contained the ileS2 transposable unit associated with IS257 on the chromosome. Three MRSA ST398-SCCmec V-t034/t4652 isolates carried ∼42 kb pSK41-like ileS2 plasmids, whereas similar ileS2 plasmids lacking tra genes were found in MRSP ST282-ΨSCCmec57395-t72/t21 isolates. Furthermore, a new group of ileS2 plasmids, carried by MRSP ST45-ΨSCCmec57395, ST433-ΨSCCmecKW21-t05 and ST2165-SCCmec IV-t06, and by one MRSA ST398-SCCmec V-t034 strain, shared the plasmid backbone with the cfr/fexA-carrying plasmid pM084526_1 in MRSA ST398. This study provides the first evidence of ileS2 integration into the S. pseudintermedius chromosome, which is a rare occurrence in staphylococcal species, and plasmids played a pivotal role in dissemination of ileS2 in both staphylococcal species.

Deep Learning-Based Automated Approach for Classifying Bacterial Images

Identifying and classifying bacterial species from microscopic images is crucial for medical applications like prevention, diagnosis, and treatment. However, because of their diversity and variability in appearance, manually classifying bacteria is difficult and time-consuming. This work suggests employing deep learning architecture to automatically categorize bacterial species in order to overcome these difficulties and raise the accuracy of bacterial species recognition. We have evaluated our suggested approach using the Digital Images of Bacteria Species (DIBaS), a publicly accessible resource of photographs of tiny bacteria. This work uses a dataset that differs in terms of bacterial morphology, staining methods, and imaging circumstances. This paper aims to enhance the accuracy and reduce the computational requirements for Convolutional Neural Networks (CNN) based classification of bacterial species using GoogLeNet and AlexNet to train the models. This paper focuses on employing transfer learning to retrain pre-trained CNN models using a dataset consisting of 2000 images encompassing 12 distinct bacteria species known to be harmful to human health. The concept of transfer learning was utilized to expedite the network's training process and enhance its categorization performance. The results are promising, with the method achieving an accuracy of 98.7% precision, recall of 99.50%, and an F1-score of 99.45% with classifier speed. Furthermore, the proposed bacteria classification approach demonstrated strong performance, irrespective of the size of the training data used. This paper contributes by automating bacterial classification to facilitate faster and more accurate identification of bacterial species, which facilitates the treatment of infections and related diseases, in addition to monitoring public health, and promoting the wise use of antimicrobial drugs. To improve outcomes in the future, researchers can also integrate deep learning techniques with other machine learning methods.

Central Line-Associated Bloodstream Infection Due to Elizabethkingia anophelis: Case Report and Literature Review on Pediatric Infections

Elizabethkingia anophelis is an opportunistic pathogen causing lifethreatening infections in humans, particularly in immunocompromised patients, neonates and the elderly. We report a case of central line-associated bloodstream infection by E. anophelis in a 2.5-year-old girl with acute lymphoblastic leukemia successfully treated with a combination of piperacillin/tazobactam and amikacin. The literature was also reviewed on pediatric infections caused by E. anophelis, focusing on clinical manifestations, underlying medical conditions, treatment and outcome. Accurate identification with MALDI-TOF, or using molecular techniques, is of the utmost importance because treatment and prognosis differ depending on the species. Considering that E. anophelis is multiresistant to antibiotics and that inappropriate antimicrobial therapy is an independent risk factor for mortality, the early, accurate identification of bacterial species and prompt effective treatment are essential to achieve optimal therapeutic outcomes.

Molecular and phenotypic identification of bacterial species isolated from cows with mastitis from three regions of Poland

BackgroundBovine mastitis is a widespread disease affecting dairy cattle worldwide and it generates substantial losses for dairy farmers. Mastitis may be caused by bacteria, fungi or algae. The most common species isolated from infected milk are, among others, Streptococcus spp., Escherichia coli, Staphylococcus aureus and non-aureus staphylococci and mammaliicocci. The aim of this paper is to determine the frequency of occurrence of bacterial species in milk samples from cows with mastitis from three regions of Poland: the north-east, the south-west and the south. To this end 203 milk samples taken from cows with a clinical form (CM) of mastitis (n = 100) and healthy animals (n = 103) were examined, which included culture on an appropriate medium followed by molecular detection of E. coli, S. aureus, Streptococcus agalactiae and Streptococcus uberis, as one of the most common species isolated from mastitis milk.ResultsThe results obtained indicated that S. uberis was the most commonly cultivated CM species (38%, n = 38), followed by S. aureus (22%, n = 22), E. coli (21%, n = 21) and S. agalactiae (18%, n = 18). Similar frequencies in molecular methods were obtained for S. uberis (35.1%) and S. aureus (28.0%). The variation of sensitivity of both methods may be responsible for the differences in the E. coli (41.0%, p = 0.002) and S. agalactiae (5.0%, p = 0.004) detection rates. Significant differences in composition of species between three regions of Poland were noted for E. coli incidence (p < 0.001), in both the culture and molecular methods, but data obtained by the PCR method indicated that this species was the least common in north-eastern Poland, while the culture method showed that in north-eastern Poland E. coli was the most common species. Significant differences for the molecular method were also observed for S. uberis (p < 0.001) and S. aureus (p < 0.001). Both species were most common in southern and south-western Poland.ConclusionsThe results obtained confirm the need to introduce rapid molecular tests for veterinary diagnostics, as well as providing important epidemiological data, to the best of our knowledge data on Polish cows in selected areas of Poland is lacking.

Carbapenemase genes in clinical and environmental isolates of Acinetobacter spp. from Quito, Ecuador.

Carbapenem-resistant Acinetobacter spp. is associated with nosocomial infections in intensive care unit patients, resulting in high mortality. Although Acinetobacter spp. represent a serious public health problem worldwide, there are a few studies related to the presence of carbapenemases in health care facilities and other environmental settings in Ecuador. The main aim of this study was to characterize the carbapenem-resistant Acinetobacter spp. isolates obtained from four hospitals (52) and from five rivers (27) close to Quito. We used the disc diffusion and EDTA sinergy tests to determine the antimicrobial susceptibility and the production of metallo β-lactamases, respectively. We carried out a multiplex PCR of gyrB gene and the sequencing of partial rpoB gene to bacterial species identification. We performed molecular screening of nine carbapenem-resistant genes (blaSPM, blaSIM, blaGIM, blaGES, blaOXA-23, blaOXA-24, blaOXA-51, blaOXA-58, and blaOXA-143) by multiplex PCR, followed by identification using sequencing of blaOXA genes. Our findings showed that carbapenem-resistant A. baumannii were the main species found in health care facilities and rivers. Most of the clinical isolates came from respiratory tract samples and harbored blaOXA-23, blaOXA-366, blaOXA-72, blaOXA-65, blaOXA-70, and blaOXA-143-like genes. The river isolates harbored only the blaOXA-51 and probably blaOXA-259 genes. We concluded that the most predominant type of carbapenem genes among isolates were both blaOXA-23 and blaOXA-65 among A. baumannii clinical isolates.

The overlooked evolutionary dynamics of 16S rRNA revises its role as the “gold standard” for bacterial species identification

The role of 16S rRNA has been and largely remains crucial for the identification of microbial organisms. Although 16S rRNA could certainly be described as one of the most studied sequences ever, the current view of it remains somewhat ambiguous. While some consider 16S rRNA to be a variable marker with resolution power down to the strain level, others consider them to be living fossils that carry information about the origin of domains of cellular life. We show that 16S rRNA is clearly an evolutionarily very rigid sequence, making it a largely unique and irreplaceable marker, but its applicability beyond the genus level is highly limited. Interestingly, it seems that the evolutionary rigidity is not driven by functional constraints of the sequence (RNA–protein interactions), but rather results from the characteristics of the host organism. Our results suggest that, at least in some lineages, Horizontal Gene Transfer (HGT) within genera plays an important role for the evolutionary non-dynamics (stasis) of 16S rRNA. Such genera exhibit an apparent lack of diversification at the 16S rRNA level in comparison to the rest of a genome. However, why it is limited specifically and solely to 16S rRNA remains enigmatic.

Multiplex Detection of Foodborne Pathogens using 3D Nanostructure Swab and Deep Learning-Based Classification of Raman Spectra.

Proactive management of foodborne illness requires routine surveillance of foodborne pathogens, which requires developing simple, rapid, and sensitive detection methods. Here, a strategy is presented that enables the detection of multiple foodborne bacteria using a 3D nanostructure swab and deep learning-based Raman signal classification. The nanostructure swab efficiently captures foodborne pathogens, and the portable Raman instrument directly collects the Raman signals of captured bacteria. a deep learning algorithm has been demonstrated, 1D convolutional neural network with binary labeling, achieves superior performance in classifying individual bacterial species. This methodology has been extended to mixed bacterial populations, maintaining accuracy close to 100%. In addition, the gradient-weighted class activation mapping method is used to provide an investigation of the Raman bands for foodborne pathogens. For practical application, blind tests are conducted on contaminated kitchen utensils and foods. The proposed technique is validated by the successful detection of bacterial species from the contaminated surfaces. The use of a 3D nanostructure swab, portable Raman device, and deep learning-based classification provides a powerful tool for rapid identification (≈5 min) of foodborne bacterial species. The detection strategy shows significant potential for reliable food safety monitoring, making a meaningful contribution to public health and the food industry.

Preliminary Identification of Bacterial Species Contaminating Okra Fruits in Some Selected Markets in Owo, Nigeria

In spite of Okra (Abelmoschus esculentus L.) cultivation relevance in the society, management of its post-harvest disease has stand out as major issue to plant pathologists. This study therefore reports findings on the spoilage bacteria associated with Okra fruit during post-harvest storage. Okra sample was purchased from three (3) local markets (Ogwagbe market, Areghona market and Oba market) in Owo local government and taken to the Plant Pathology Laboratory of the Department of Crops Soil and Pest Management, Federal University of Technology, Akure. About 2g of deteriorated Okra fruit sample was sterilized and aseptically transfer into the sterile 20cm2 beaker. The bacteria isolated were incubated at 37+ 20c for 24hours in a Nutrient Agar (NA) plate. At the end of incubation period the Colonies forming units from violet bacteria cells were counted and recorded appropriately per gram of each of the deteriorating Okra sample. Pure culture of individual isolates was kept at 40c for biochemical test and isolates were identified. A total of 26 bacteria were isolated and identified from the Okra sample from the 3 local markets on the basis of colony morphology and the staining characteristics. Location A has the highest population of bacteria isolate while location B and C had lowest bacterial population. The highest occurring genera can be found in Micrococcus, Bacillus and Staphylococcus followed by Alcaligenes, Pediococcus, and Erwinia. Alcaligenes odorans and Bacillus pumilus are the most occurring species of bacteria isolated from the market. Total viable counts ranges from 1.20 X 10-8 (cfu/g) to 1.72 X 10-8 (cfu/g). The highest average coliform forming unit occurs in Location A (1.52 X 10-8 (cfu/g)) while the least average coliform forming unit occurred in Location B (1.23 X 10-8 (cfu/g)). Alcaligenes odorans Bacillus pumilus and Micrococcus spp. had the highest frequency of occurrence (67 %). The presence of these bacteria on Okra fruit are potential threat to its production most importantly coliforms, pose a serious threat to consumers' health as the bacteria could produce toxins, which are poisonous when consumed. Proper handling methods should be adopted by both farmer and consumers to minimize the bacterial deterioration of okra fruit in the study area.

Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing

The plant microbiome is crucial for plant growth, yet many important questions remain, such as the identification of specific bacterial species in plants, their genetic content, and location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice-phyllosphere, we perform a metagenomic analysis using long-read sequences. Here, 1.8 Gb reads are assembled into 26,067 contigs including 142 circular sequences. Within these contigs, 669 complete 16S rRNA genes are clustered into 166 bacterial species, 121 of which show low identity (<97%) to defined sequences, suggesting novel species. The circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs are defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of a difficult-to-culture bacterium Candidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.

Antibiotic Resistance Trends Among Enterobacteriaceae in Saudi Arabia: A Systematic Review.

Antibiotic resistance is a global public health concern that poses a significant threat to the effective treatment of bacterial infections. Enterobacteriaceae, a family of gram-negative bacteria, are associated with a wide range of infections, including urinary tract infections, bloodstream infections, and respiratory tract infections. This systematic review aimed to examine the antibiotic resistance trend among Enterobacteriaceae in Saudi Arabia in the period between 2003 and 2023. Five databases (PubMed, Medline, Ovid, Scopus, and Cochrane) were searched using the keywords "Resistance AND Enterobacteriaceae AND Saudi Arabia" in the title and abstract. All papers assessing the prevalence of resistance among Enterobacteriaceae in Saudi Arabia were included in the systematic review. Out of 97 papers that were extracted through the database search,22 articles were considered suitable for the systematic review. The articles included 17027 Enterobacteriaceae isolates, out of which 7592 isolates were identified as resistant bacteria. The studies included various resistant strains, such as Escherichia coli and Klebsiella pneumoniae, that were responsible for various clinical conditions, including urinary tract infections, blood infections, surgical site infections, and pneumonia. In addition, the review highlighted the dynamic nature of antibiotic resistance, with the identification of new resistant bacterial species and the emergence of resistance to newer antibiotic classes over the last decade. Continued surveillance, rational antibiotic use, and the development of alternative treatment options are crucial to address the evolving landscape of antibiotic resistance among Enterobacteriaceae bacteria in the country.

Molecular Characterization of Extended Spectrum β-Lactamase-Producing Escherichia coli: Insights into the O25b-ST131 Clone in Mexican Urinary Tract Infections

Background: The urgent need for antimicrobial research to address the escalating global challenge of β-lactam antibiotic resistance, particularly in Escherichia coli-induced urinary tract infections (UTI), is underscored by the increasing resistance to ciprofloxacin in Latin America. This issue has led to a heightened dependence on alternative therapeutics, such as cephalosporins. The identification of extended-spectrum β-lactamase (ESBL)-producing E. coli, notably the O25b-ST131 clone, adds complexity to UTI management. The prevalence of ESBL-producing E. coli varies globally due to factors including regional antimicrobial usage practices. Objectives: The goal of this study was to identify and molecularly characterize ESBL-producing E. coli isolates to identify the pandemic O25b-ST131 clone related to UTIs in one healthcare institution in Mexico. Methods: Bacterial species identification and antibiotic susceptibility tests were performed using the VITEK 2. The ESBL genes were identified using polymerase chain reaction (PCR). The E. coli genotyping was carried out by the phylogenetic group analysis and the O25b-ST131 identification. Results: A total of 86 unique E. coli isolates were confirmed as ESBL, and 75% were obtained from UTIs. The most prevalent β-lactamase genes were blaCTX-M (66%), blaTEM (8.1%), blaCTX-M/SHV (5.8%), blaCTX-M/TEM (4.6%), and blaSHV (2.3%). The B2 phylogroup was most prominent (54.4%), with 46.5% identified as a globally pandemic O25b-ST131 clone. No evident relationship was observed using random amplified polymorphic DNA (RAPD) between nosocomial and community-acquired infections in ESBL-producing E. coli isolates. Conclusions: The obtained findings highlight the significance of monitoring molecular epidemiology in antibiotic resistance profiles of the O25b-ST131 E. coli clone.