Identification Of Bacteria Research Articles

Identifying a Biocontrol Bacterium with Disease-Prevention Potential and Employing It as a Powerful Biocontrol Agent Against Fusarium oxysporum

Biocontrol microbes are environment friendly and safe for humans and animals. To seek biocontrol microbes effective in suppressing Fusarium oxysporum is important for tomato production. F. oxysporum is a soil-borne pathogen capable of causing wilt in numerous plant species. Therefore, we found a biocontrol bacterium with an excellent control effect from the rhizosphere soil of plant roots. In this work, we focus on two parts of work. The first part is the identification and genomic analysis of the biocontrol bacterium Y-4; the second part is the control efficiency of strain Y-4 on F. oxysporum. For this study, we identified strain Y-4 as Bacillus velezensis. It is an aerobic Gram-positive bacterium that can secrete a variety of extracellular enzymes and siderophores. Strain Y-4 also contains a large number of disease-resistant genes and a gene cluster that forms antibacterial substances. In addition, we found that it significantly inhibited the reproduction of F. oxysporum in a culture dish. In the indoor control effect test, after treatment with strain Y-4 suspension, the disease index of tomato plants decreased significantly. Furthermore, the control efficiency of the plants was 71.88%. At the same time, Y-4 bacterial suspension induced an increase in POD and SOD enzyme activities in tomato leaves, resulting in increased plant resistance. Taken together, strain Y-4 proves to be an effective means of controlling F. oxysporum in tomatoes.

Sheath-enhanced concentration and on-chip detection of bacteria from an extremely low-concentration level.

Microfluidic-based sheath flow focusing methods have been widely used for efficiently isolating, concentrating, and detecting pathogenic bacteria for various biomedical applications due to their enhanced sensitivity and exceptional integration. However, such a microfluidic device usually needs complicated device fabrication and sample dilution, hampering the efficient and sensitive identification of target bacteria. In this study, we develop and fabricate a sheath-assisted and pneumatic-induced nano-sieve device for achieving the improved on-chip concentration and sensitive detection of Staphylococcus aureus (MRSA). The optimized nanochannel design with diverging configuration is beneficial to the regulation of the hydrodynamic flow while the sheath flow is focusing the sample to the confined region as expected. Per the experimental finding, a high flow ratio (sheath flow/sample flow) presents enhanced target concentration by comparing with a low flow ratio. With this setup, MRSA bacteria with an extremely low concentration of ∼100 CFU mL-1 are successfully and sensitively detected under a fluorescence microscope, less than 30 min, demonstrating a reliable sheath-enhanced concentration and on-chip detection for target bacteria. Additionally, the theoretical model introduced here further rationalizes the working principle of our nano-sieve device, potentially guiding the optimization of next generation devices for highly sensitive and accurate on-chip bacteria detection at a much lower concentration level below 100 CFU mL-1.

Enzyme-Responsive Chitosan-Based Electrospun Nanofibers for Enhanced Detection of β-Glucuronidase from Pathogenic E. coli

Antimicrobial resistance (AMR) poses a significant global health challenge, leading to the ineffectiveness of numerous conventional antibiotics against various bacterial infections. Hence the rapid detection and identification of pathogenic bacteria are imperative for managing AMR and implementing suitable treatment approaches. To improve rapid detection, a biopolymer-based autonomously reporting enzyme-sensitive biopolymer material has been developed for detecting β-glucuronidase (β-Gus) from pathogenic E. coli. In the presence of enzyme β-Gus a blue-colored fluorophore is released from functionalized electrospun chitosan-polyethylene oxide nanofibers, which is monitored via fluorescence spectroscopy. The nanofibers exhibited a 3.4 times enhanced sensitivity compared to neat hydrogels and also to related chromogenic sensing materials. For an observation time of 60 minutes, a limit of detection (LOD) for β-Gus was determined to be 4.7 nM. This nanofiber sensing substrate was then studied with the pathogenic E. coli strain NCTC 10418, showing a three times greater sensitivity compared to the hydrogel substrate. These results are attributed to a larger surface to volume ratio of the electrospun chitosan nanofibers compared to the neat swollen hydrogel.

Isolation, Identification and Antibiogram of Bacteria from Imported Frozen Fish at Public Markets in Mosul City, Iraq

Isolation, Identification and Antibiogram of Bacteria from Imported Frozen Fish at Public Markets in Mosul City, Iraq

Whole-cell aptamer-based techniques for rapid bacterial detection: Alternatives to traditional methods.

Controlling the spread of bacterial infectious diseases is a major public health issue, particularly in view of the pandemic of bacterial resistance to antibiotics. In this context, the detection and identification of pathogenic bacteria is a prerequisite for the implementation of control measures. Current reference methods are mainly based on culture methods, which generate a delay in obtaining a result and requires equipment. Consequently, focusing on the detection of the whole bacterium represents a very attractive alternative, since no culture is required. Several techniques have already been deployed to identify whole-cell bacteria. In recent decades, growing interest in nucleic acid aptamers has emerged as a viable alternative to antibodies as recognition elements, offering preferable stability, cost-efficiency, good specificity and affinity. This review explores current alternative methods for the detection of whole-cell bacteria, with particular emphasis on aptamer-based assays. These assays have shown promising results in various transduction mechanisms, including optical, electrochemical, and mechanical approaches, enhancing their versatility in different diagnostic platforms. The integration of aptamers in these detection methods offers rapid, sensitive, versatile and portable solutions for pathogen identification, positioning them as valuable tools in the fight against bacterial infections.

The identification of low-pathogenic bacteria on removed spinal implants and implications for antimicrobial prophylaxis

IntroductionThe role of low-pathogenic bacteria cultured from removed spinal implants is unclear and the efficacy of perioperative single-dose antibiotics against such bacteria remains underexplored. Research questionThis study aims to investigate whether pedicle screw loosening is associated with pathogens and if the choice of perioperative antibiotics can prevent these bacteria. MethodsA retrospective analysis was conducted on 93 patients with implants removed between 01/01/2018 and 03/31/2020. Patients with both loosened and non-loosened implants were included. The latter group was subdivided into cases where implants were exchanged due to adjacent segment degeneration (ASD) and those with elective implant removal after fracture healing. Bacterial cultures from removed implants were analyzed for resistance profiles against the prophylactic single-shot antibiotics administered during implantation. Patients with acute infection, spondylodiscitis, deep wound infection, empyema, and carbon/polyetheretherketone spinal implants were excluded. ResultsBacterial isolates were detected in both loosened (41%) and non-loosened (27%) implants (p=0.23). The most frequently cultivated bacteria were Cutibacterium acnes and Staphylococcus epidermidis. Sensitivity to the administered antibiotics was 75%. While Cutibacterium acnes was entirely sensitive, Staphylococcus epidermidis was completely resistant. Patients with loosened implants without bacteria had a significantly lower bone mineral density (BMD) than patients with implants removed due to ASD. However, patients with loosened implants and positive bacterial cultures had comparable BMD to ASD patients. ConclusionsThe high rate of sensitive Cutibacterium acnes and resistant Staphylococcus epidermidis on removed spinal implants suggests a need to revisit current antimicrobial prophylaxis. Further research is required to determine the clinical significance of low-virulence bacteria, especially on non-loosened implants.

Rapid Identification of Pathogenic Bacteria from Clinic Positive Blood Cultures Via Virus-like Magnetic Bead Enrichment and MALDI-TOF MS Profiling

Reducing the time required for the detection of bacteria in blood samples is a critical area of investigation in the field of clinical diagnosis. Positive blood culture samples often require...

Identification of pathogenic bacteria that associated with male infertility

Identification of pathogenic bacteria that associated with male infertility

Deep dive into the diversity and properties of rhodopsins in actinomycetes of the family Geodermatophilaceae.

In recent decades, most studies of microbial rhodopsins have focused on their identification and characterization in aquatic bacteria. In 2021, actinomycetes of the family Geodermatophilaceae, commonly inhabiting terrestrial ecosystems in hot and arid regions, have been reported to contain rhodopsins with DTEW, DTEF and NDQ amino acid motifs. An advanced bioinformatics analysis performed in this work additionally revealed NTQ rhodopsin and heliorhodopsins. The absorption maxima identified for rhodopsins from the above five groups ranged from 513nm (NTQ rhodopsin) to 559nm (heliorhodopsin). An assessment of pumping specificity showed that DTEW and DTEF rhodopsins possessed outward H+-transport activities. Ca2+ ions were required for pumping if E. coli C43(DE3) was used as an expression strain, but were unnecessary in the case of E. coli BL21(DE3). For NDQ rhodopsin, outward H+-transport was detected in NaCl and KCl solutions at pH5 and 6, but not at neutral pH. A weak Na+-efflux was observed for this rhodopsin at pH6 and 7 in a NaCl solution only in the presence of proton ionophore. NTQ rhodopsin acted as an inward Cl--, Br--, and I-- pump, with a much weaker activity towards NO3-. No pumping activity was detected for the heliorhodopsin tested. The finding of rhodopsins with novel properties further expands the rhodopsin landscape.

A xylenol orange-based pH-sensitive sensor array for identification of bacteria and differentiation of probiotic drinks.

The development of straightforward and cost-efficient methods for bacterial identification is very important. In this study, we utilized xylenol orange, metal ions, and diverse bacterial carbon sources to construct a sensor array, achieving precise bacterial identification. Initially, we examined the absorbance variations of xylenol orange with five metal ions (Mn2+, Co2+, Ni2+, Cu2+, and Zn2+) at pH levels ranging from 4 to 7, observing significant changes at 570 nm or 580 nm. Given that bacteria can generate varying amounts of acid in different carbon sources, we employed a blend of xylenol orange and the five metal ions as pH-sensitive probes to characterize bacterial metabolism in three carbon sources, resulting in the development of a five-sensor array that effectively differentiated seven bacteria. Additionally, by utilizing xylenol orange with Co2+, we successfully identified six different bacterial mixtures and five types of probiotic drink products. These findings highlight the potential of our methods for broader practical application in bacterial identification in practical use.

Persistent luminescence encoding for rapid and accurate oral-derived bacteria identification

The dysbiosis of oral microbiota contributes to diseases such as periodontitis and certain cancers by triggering the host inflammatory response. Developing methods for the immediate and sensitive identification of oral microorganism is crucial for the rapid diagnosis and early interventions of associated diseases. Traditional methods for microbial detection primarily include the plate culturing, polymerase chain reaction and enzyme-linked immunosorbent assay, which are either time-consuming or laborious. Herein, we reported a persistent luminescence-encoded multiple-channel optical sensing array and achieved the rapid and accurate identification of oral-derived microorganisms. Our results demonstrate that electrostatic attractions and hydrophobic-hydrophobic interactions dominate the binding of the persistent luminescent nanoprobes to oral microorganisms and the microbial identification process can be finished within 30 min. Specifically, a total of 7 oral-derived microorganisms demonstrate their own response patterns and were differentiated by linear discriminant analysis (LDA) with the accuracy up to 100% both in the solution and artificial saliva samples. Moreover, the persistent luminescence encoded array sensor could also discern the microorganism mixtures with the accuracy up to 100%. The proposed persistent luminescence encoding sensor arrays in this work might offer new ideas for rapid and accurate oral-derived microorganism detection, and provide new ways for disease diagnosis associated with microbial metabolism.

Application of Biofire Filmarray Joint Infection Panel for Rapid Identification of Aetiology in a Necrotizing Fasciitis Case.

Background: Monomicrobial Enterobacterales necrotizing fasciitis is associated with exceedingly high mortality rates. Although effective antimicrobial therapy is an important part of treatment, the traditional microbiological diagnostic methods are not fast enough to meaningfully influence early therapeutic decisions. Methods: Here, we report the application of the BioMérieux Biofire Filmarray Joint Infection Panel (BFJIP) for the rapid detection of the causative agent and susceptibility prediction in such a case. Aside from the BFJIP-based rapid diagnostic approach and culturing, the whole genome sequencing (WGS) of the causative agent was performed using Illumina MiSeq and Oxford Nanopore MinION platforms. Results: The BFJIP indicated the presence of K. pneumoniae, without KPC, VIM, IMP, NDM, OXA-48 carbapenemase genes, and CTX-M-type extended-spectrum beta-lactamases. Based on the WGS data, the isolate belonged to the K1-capsule-type ST23, harboured a pNTUH-2044-like plasmid, and was positive for all the virulence factors associated with this lineage. The conventional susceptibility results were also in accordance with the BFJIP results; the isolate lacked any of these acquired resistance mechanisms. Conclusions: Despite this being the first case of the successful identification of pathogenic bacteria in necrotising fasciitis using this assay, the BFJIP may become a useful tool for rapid identification of pathogens in necrotising fasciitis cases and guiding antimicrobial therapy for better clinical outcomes.

Prevalence of Escherichia coli and Salmonella in Drinking Water around Sher-e-Bangla Agricultural University Campus

Microbial contamination of drinking water poses a health threat for man and animals. The aim of this study was to detect Escherichia coli (E. Coli) and Salmonella in drinking water from the Sher-e-Bangla Agricultural University (SrAU) campus and its surrounding areas between January 2021 and August 2021. A total of 60 water samples were collected from dormitories, academic buildings and nearby shopping centres. Identification of bacteria was done using growth characteristics on selective media, staining, microscopic examination, and biochemical tests. The overall prevalence of contamination was 53.3%, with the highest rate (61.1%) in water from shopping centres. Drinking water in the SrAU campus and its vicinity is unsafe for drinking and household purposes. Sanitation programmes of the SrAU health centre need to be strengthen to mitigate health risks of the community. Bang. vet. 2024. Vol. 41, No. 1 – 2, 1 – 6

Assessment of Bacteriological Quality and Identification of Chlorine-Tolerant Bacteria from Different Potable Water Sources in Girei, Nigeria

Domestic water sources such as wells, taps, and rivers are often used for drinking, cooking, and other household purposes, particularly in rural and peri-urban areas however in most places, their microbiological quality is not always ensured. In this study, 45 water samples were collected from key domestic water sources; 20 each from wells and taps, and 5 from River Benue in Girei, Nigeria following standard sampling techniques. Total aerobic bacterial count (in CFU/mL) for each sample was determined and river water had the highest average microbial count (285), followed by well water (248), and tap water had the lowest count (181). Identification of isolates involved cultural characteristics, Gram staining, motility, and biochemical tests. Bacterial species associated with the water sources were Acinetobacter sp., Aeromonas sp., Bacillus subtilis, Citrobacter, Escherichia coli, Enterococcus faecalis, Enterobacter sp., Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus sp., Providencia sp., Staphylococcus aureus, Staphylococcus epidermidis, Salmonella sp. and Serratia sp.. Chlorine tolerant isolates were determined after treating each sample with 9.9 mg/L (9.9 ppm) of Sodium hypochlorite (NaOCl) at a contact time of 30 minutes. They include 13 isolates from 9 genera, viz: Acinetobacter sp., B. subtilis, Citrobacter sp., E. coli, Enterobacter sp., K. pneumoniae, P. aeruginosa, Proteus sp. and Serratia sp. By subjecting the treatment tolerant isolates to higher concentrations of NaOCl, results indicated that high concentrations are required to neutralize the isolates with the highest bactericidal concentration observed in B. subtilis (70 ppm), and the lowest was 40 ppm observed in Serratia sp. and E. coli. The findings highlight significant bacterial contamination in water sources, some of which are pathogenic and chlorine-tolerant, emphasizing the need for proper water treatment methods, such as boiling, before consumption by residents. Stam. J. Microbiol. 2024;14(1):5-12

Isolation and Identification of Chromium-Tolerant Bacteria from Poultry Litter in Dhaka, Bangladesh

Tannery waste, known for its high chromium content, often contaminates chicken feed, accumulating chromium in chickens and their excreted waste. This study aimed to isolate chromium-tolerant bacteria from chicken litter and evaluate their ability to withstand various chromium concentrations. Four bacterial isolates—CM3, CM4, CM5, and CM6 were presumptively identified as Pseudomonas sp., Bacillus sp., Staphylococcus sp., and Bacillus sp., respectively. The isolate CM4 showed the highest tolerance, growing at 800 mg/L concentrations. A subsequent experiment focused on CM4, where growth was measured by absorbance at 600 nm across chromium concentrations from 0 mg/L to 3200 mg/L. The results indicated a significant decrease in growth with increasing chromium levels, with near-complete inhibition at the highest concentrations. This study highlights the potential of chromium-tolerant bacteria from poultry litter for bioremediation, particularly in environments contaminated with this heavy metal. These findings contribute to ongoing efforts to mitigate chromium pollution through microbial interventions. Stam. J. Microbiol. 2024;14(1):18-21

Site-selective modifications by lipid A phosphoethanolamine transferases linked to colistin resistance and bacterial fitness.

Rising levels of resistance to increasing numbers of antimicrobials have led to the revival of last resort antibiotic colistin. Unfortunately, resistance to colistin is also spreading in the form of mcr genes, making it essential to (i) improve the identification of resistant bacteria to allow clinicians to prescribe effective drug regimens and (ii) develop new combination therapies effective at targeting resistant bacteria. Our results demonstrate that PETs, including MCR variants, are site-selective in Escherichia coli and that site-selectivity correlates with the level of susceptibility and fitness costs conferred by certain PETs. Site selectivity associated with a given PET may not only help predict colistin resistance phenotypes but may also provide an avenue to (i) improve drug regimens and (ii) develop new combination therapies to better combat colistin-resistant bacteria.

Isolation and Molecular Identification of Lipolytic Bacteria from Oil Contaminated Soil

Isolation and Molecular Identification of Lipolytic Bacteria from Oil Contaminated Soil

Updating the Relationship Between the Threshold Value of Average Nucleotide Identity and Digital DNA-DNA Hybridization for Reliable Taxonomy of Corynebacterium.

Currently, bacterial classification at the species level relies on the 95-96% average nucleotide identity (ANI) value that is known to be equivalent to a 70% digital DNA-DNA hybridization (dDDH) value. However, during the routine identification of bacteria in the uteri of camels with a history of conception failure, we found that four out of the seven strains (2298A, 2569A, 2652, 2571B, 1103A, 2571A, and 335C) could not be assigned to any valid Corynebacterium species. Furthermore, a 70% dDDH value did not correspond to a 95-96% ANI value in strain 2569A. Thus, we aimed to classify these strains and explain the mechanisms underlying gene repertoire diversity and the disagreement we found between the ANI and dDDH cutoff values. For this study, we extracted information from the genomes of 150 Corynebacterium-type species and seven sequenced genomes of uterine Corynebacterium isolates. We found that the 96.67% OrthoANI value should be used in place of the generally accepted 95-96% ANI threshold in order to obtain an equivalent 70% dDDH value. Phylogenomic analysis determined the evolutionary position of each uterine strain. Then, strains 2652 and 2571B were classified as C. camporealensis based on the ANI value (98.44% and 98.72%) and dDDH value (85.8% and 88.5%). Strain 2569A had a 96.58% ANI and a 69.4% dDDH value and was classified as C. urogenitale. The strains 335C, 1103A, 2571A, and 2298A were classified as novel Corynebacterium based on the ANI value (77.12, 94.01%, 94.26%, and 94.03%) and dDDH value (21.3%, 54.1%, 54.9%, and 51.3%), respectively. Genes for menaquinone biosynthesis and the saturation of chains were detected in uterine strains and their closely related type strains. Gene gain predominates as a source of variation in the gene repertoire. Most of these genes are gained by horizontal gene transfer, driven by genomic islands and prophage. In summary, we refined the ANI cutoff value for an accurate diagnosis of Corynebacterium. Moreover, we clarified the mechanism underlying the diversity of the gene repertoire and expanded the number of Corynebacterium species isolated from the camel uterus.

Investigating of Some Virulence Genes of Salmonella Isolated From Chickens and Their Eggs Using Biochemical and Molecular Method

This investigation aimed for isolation and molecularly identify of Salmonella species from local chickens and their eggs. A total of four chicken flocks located inside Baghdad's urban limits provided the 100 cloacal swabs and 100 egg shells used to isolate Salmonella spp. These were cultured on basic medium, then subcultured on XLD then biochemical tests were done for identification of bacteria. PCR was done for confirmation of the results by using the three genes flic, rfbsp,and rfbsg. After t confirming he presence of Salmonella spp., the Kirby-Bauer disc diffusion assay was used to determine susceptibility of antibiotics in all of the isolates (16). The antibiotics that were included in the test were from Bioanalyse in Turkey and included the following: Trimethoprime & Sulphamethoxazole (25 µg), Azithromycin (15 µg), Florfenicol (30 µg), Gentamycin (10 µg), Ciprofloxacin (5 µg), Ampicillin (10 µg), and Tetracycline (30 g). The current results showed that Salmonella spp. was isolated from cloacal swabs at 15% while from egg shell the percentage was 2% and the total percentages of isolation was 8.5%. The genes flic and rfbsg had been were also found in all isolates. The investigation found the following antibiotic resistance rates among the isolates: Azithromycin (82.3%), Florfenicol (70.6%), Trimethoprime- Sulphamethaxezole (70.6%), Tetracycline (64.7%), Ciprofloxacin (58.8%), Ampicillin (52.3%), and Gentamycin (35.3%) Salmonella spp. was isolated significantly from cloacal swabs compared to eggshell which was characterized by multidrug resistance.

Unveiling bisphenol A-degrading bacteria in activated sludge through plating and 13C isotope labeled single-cell Raman spectroscopy.

Bacteria play a crucial role in biodegradation of recalcitrant endocrine-disrupting compounds (EDCs), such as bisphenol A (BPA). However, in-situ identification of BPA-degrading bacteria remains technically challenging. Herein, we employed a conventional plating isolation (PI) and a new single cell Raman spectroscopy coupled with stable isotope probing (Raman-SIP) approach to enrich and identify BPA-degrading bacteria from activated sludge (AS). AS-inhabitant bacteria were exposed to either 12C-BPA or 13C-BPA as sole carbon source over three consecutive generations. While PI relies on colony proliferation on agar media, Raman-SIP enables identification of in situ BPA-degrading bacteria in a culture-independent way. The results showed that BPA dissipation correlated with increased bacterial growth. The uptake of 13C-BPA by single cells was verified by Raman spectra, suggesting occurrence of both metabolic and biosynthesis processes. This direct tracking of the fate of 13C-BPA within cells highlights the advantages of Raman-SIP over PI technique. PI isolated four BPA-degrading bacterial strains belonging to Comamonas, Pseudomonas, and Herbaspirillum genera. Meanwhile, Raman-SIP identified labeled cells belonging to Comamonas and Pseudomonas genera. Metagenomics of labeled cells revealed the presence of fifteen genes associated with benzene ring cleavage. This study provides a novel Raman-SIP approach for detecting and characterizing BPA-assimilating bacteria at a single cell level.