Progress In Microbes & Molecular Biology

Genomic and Resistome Analyses of Elizabethkingia anophelis Strain B2D isolated from Dental Plaque of Patient

2024-04-17T15:30:10+08:00

In this study, strain B2D isolated from a dental plaque sample of a human patient was studied for its general characteristics, taxonomic identification, genome features, and resistome profile. The bacterium exhibited antibiotic resistance to all beta-lactam antibiotics, nitrofuran, and sulfonamides, with high minimum inhibitory concentrations. It was only sensitive to the fluoroquinolone ciprofloxacin and intermediately susceptible to aminoglycoside tobramycin. A preliminary identification through 16S rRNA gene sequences revealed that it shared the highest sequence identity with Elizabethkingia anophelis subsp. endophytica JM-87^T (100%) and Elizabethkingia anophelis subsp. anophelis R26^T (99.31%). The draft genome of strain B2D was approximately 3.9 Mbp with 50 contigs and 35.5% GC content. A 16S rRNA gene and core genes-based phylogenetic analyses revealed a close phylogenetic relationship between strain B2D and the other Elizabethkingia type strains. An above species level threshold average nucleotide identity value confirmed its taxonomic identity as Elizabethkingia anophelis. Furthermore, we conducted a resistome analysis of strain B2D and Elizabethkingia type strains, revealing the presence of widespread antibiotic resistance genes, including beta-lactamases and genes associated with cationic antiseptic resistance and glycopeptide resistance. Overall, the multidrug resistant profile of strain B2D as elucidated and confirmed through whole genome analysis indicated its potential as a reservoir of beta-lactamase genes. Moreover, its presence within dental plaque in the human oral cavity prompts speculation regarding its role as an opportunistic pathogen capable of causing infections, particularly in immunocompromised individuals.

Environmental Metagenomic Analysis of "ESKAPE" Pathogens in the Pediatric Intensive Care Unit of General Hospital Yogyakarta Indonesia

2023-09-05T01:28:27+08:00

Healthcare-associated infections (HAIs) are infections that occur while receiving health care, develop in a hospital or other healthcare facility, and first appear 48 hours or more after hospital admission, or within 30 days after having received health care. HAIs are linked to high mortality rates, prolonged stays, increased hospital overhead costs, and financial burdens on patients. Bacterial transmission from medical personnel or the environment, or patient-to-patient contact are all potential causes of these infections. A molecular epidemiology approach is needed to examine the contribution of risk factors and the distribution of "ESKAPE" pathogens within the hospital environment. In this study, we conducted a comprehensive analysis of the distribution of ESKAPE bacterial pathogens in the environment of pediatric intensive care units over a 30-day time interval using shotgun metagenomics. We collected samples from handwashing sinks, the floor around patients, and ventilator screens and tubes in the pediatric intensive care unit (PICU) of General Hospital, Yogyakarta, Indonesia in March 2022. We determine taxonomic profiles and also detect resistome, and virulome distribution of ESKAPE pathogens on various environmental surfaces through shotgun metagenomic sequencing. The microbiomes of the floor, sink, and mechanical ventilator exhibit a diverse composition of microbial communities, featuring significant species richness based on Shannon and Simpson’s index. These microbiomes encompass a wide array of microbial species, including ESKAPE bacterial pathogens, as well as profiles related to resistome and virulome. ESKAPE pathogens, especially Acinetobacter baumannii, predominated in the PICU environment. Most virulome have been associated with metabolism/nutrition and adhesion. Noteworthy findings include resistome genes characterized by mechanisms like efflux pumps (MDR) and alterations in antibiotic targets.

Lutein Suppresses the Maturation and Function of Bone Marrow-Derived Dendritic Cells

2024-04-18T12:59:09+08:00

Lutein, nonivamide, and baicalein, organic compounds found in a variety of plants, are known to exert anti-inflammatory effects in animal cells. Dendritic cells (DCs) are professional antigen-presenting cells (APCs) and link the innate and adaptive immune systems. DCs can be directed into fully mature APCs by exposure to bacterial or viral components, resulting in inflammatory situations. The manipulation of DC maturation provides a strategy for the treatment of allergic and inflammatory diseases. In this study, we evaluated the effects of lutein, nonivamide, and baicalein on the maturation and activation of DCs. Compared to nonivamide and baicalein, lutein significantly and dose-dependently reduced the levels of maturation-associated cell surface markers, including CD40, co-stimulatory molecule CD86, and major histocompatibility complex class II (I-A^b) molecule in lipopolysaccharide (LPS)-stimulated DCs. Lutein also decreased IL-12p40 and IL-6 gene expression and secretion in LPS-stimulated DCs. Furthermore, lutein significantly enhanced the endocytic ability of LPS-stimulated DCs. These results demonstrated that lutein may exhibit immunosuppressive activity by inhibiting the phenotypic and functional maturation of DCs, and provide new evidence for the value of lutein in the search for novel therapeutic agents in the treatment of inflammatory diseases.

Purification of Anti-Mycobacterium tuberculosis MPT64 Immunoglobulin-Y from Egg-Yolk Supernatant Using Thiophilic Adsorption Chromatography

2023-11-21T10:27:29+08:00

The significance of immunoglobulin Y (IgY) as a particular antibody equal to mammalian IgG is well understood. However, due to a lack of reliable purification procedures, producing highly pure IgY remains problematic. In this study, we aimed to optimize the recovery of pure IgY anti-MPT64 using thiophilic adsorption chromatography. The purification of IgY anti-MPT64 was achieved by initial PEG lipid precipitation, then an optimized purification by varying the gradient concentration of elution buffer into five steps gradient (0-20, 20-40, 40-60, 60-80, and 80-100%v/v) for three injection column volume (CV) each and two steps gradient (0-50 and 50-100%v/v) in eight CV for each concentration. The obtained IgY was characterized by SDS-PAGE and dot-blot then determined its content levels using the Lowry method. The results showed that the five steps gradient purification was found to provide a better purity level of IgY than the two steps gradient. However, the IgY content obtained in the two steps gradient purification (2.2632± 0.011 mg/mL) was higher than the five steps gradient purification (1.35482 ± 0.023 mg/mL). Nevertheless, both purified IgY results can recognize MPT64 protein through a dot blot test. Therefore, it can be summarized that thiophilic adsorption chromatography with five steps gradient of purification was an efficient process to obtain a higher purity of IgY anti-MPT64, especially to be targeted as a diagnostic kit component for MPT64 detection.

Complete Whole-Genome Sequence of Streptomyces sp. MUM 178J, a Potential Anti-Vibrio Agent

2024-02-16T14:25:27+08:00

Streptomyces sp. is a group of filamentous, Gram-positive bacteria notoriously known for their capabilities in producing bioactive compounds that have been used as novel drugs and lead in drug development. The Streptomyces sp. MUM 178J was isolated from a mangrove forest in Malaysia. This isolate was found to harbor anti-Vibrio properties as its crude extract inhibited the growth of multidrug-resistant Vibrio parahaemolyticus. Therefore, the strain was subjected to whole genome sequencing to unearth its genomic potential. The genome of Streptomyces sp. MUM 178J consists of 6,699,249 bp with a G+C content of 71.3%. 66 tRNA genes and 18 rRNA genes were also predicted to be present within the genome. Further analysis with the bioinformatics tool, antiSMASH (antibiotics & Secondary Metabolite Analysis Shell), detected nine biosynthetic gene clusters displaying more than 70% similarity to known gene clusters, including one associated with melanin production. Melanin has demonstrated antagonistic activity against the growth of members of the Vibrio family, including V. parahaemolyticus. This indicates the potential correlation between the production of melanin and the anti-Vibrio properties of MUM 178J. The availability of the whole genome sequence of Streptomyces sp. MUM 178J allows for future in-depth investigation and potential exploitation of MUM 178J to harvest useful bioactive compounds.