Metagenomic data reveals microbiome characteristics of culture-negative brain abscess samples.

A brain abscess is a focal collection of pus in the brain parenchyma surrounded by a well-vascularized collagenous capsule in response to an infection. The microbiome of brain abscesses has been shown to be polymicrobial, dominated by uncultivable and anaerobic organisms of odontogenic origin. The data provided in this article includes the sequences of bacterial 16S rRNA gene from three culture-negative brain abscess samples suspected to have poly-microbial aetiology based on Sanger sequencing. DNA was extracted from brain abscess samples, and targeted-metagenomics sequencing was done by amplifying the full-length bacterial 16S rRNA followed by a nested PCR for V3-V4 regions using universal and specific primers. The barcoded amplicons were sequenced on Illumina MiSeq V2 instrument to generate 0.5M, 250bp paired-end reads/sample. The total sequencing reads were 455966, 345746, and 438658 for samples P32, P49, and P8, respectively. Bioinformatics tools such as FLASH, VSEARCH, and QIIME1 were used to process the reads generated for Operational Taxonomic Unit analysis (OTU). Bacterial species belonging to phyla Firmicutes, Bacteroidetes, and Fusobacteria were abundant in samples P49 and P8, which are mainly anaerobic and microaerophilic bacteria. These are typical of the human oral/gut microbiota and are implicated in brain abscess formation. Sample P32 showed the abundance of bacterial species belonging to phyla Proteobacteria and Actinobacteria, which are commonly found in the environment. Raw data files are available at the Sequence Read Archive (SRA), National Center for Biotechnology Information (NCBI), and data information can be found at the BioProject, PRJNA785100 under the accession numbers SRX13271109, SRX13271110, SRX13295897. The data shows the microbiome constitution, including several anaerobic and unculturable bacterial species from culture-negative brain abscess samples. This dataset will be useful for future research on comparative genomics and management of patients with culture-negative brain abscesses.

Metagenomic data of bacterial community from different land uses at the river basin, Kelantan.

The data provided in the article includes the sequence of bacterial 16S rRNA gene from a high conservation value forest, logged forest, rubber plantation and oil palm plantation collected at Kelantan river basin. The logged forest area was previously notified as a flooding region. The total gDNA of bacterial community was amplified via polymerase chain reaction at V3-V4 regions using a pair of specific universal primer. Amplicons were sequenced on Illumina HiSeq paired-end platform to generate 250 bp paired-end raw reads. Several bioinformatics tools such as FLASH, QIIME and UPARSE were used to process the reads generated for OTU analysis. Meanwhile, R&D software was used to construct the taxonomy tree for all samples. Raw data files are available at the Sequence Read Archive (SRA), NCBI and data information can be found at the BioProject and BioSample, NCBI. The data shows the comparison of bacterial community between the natural forest and different land uses.

Recombinant LipL32 Protein Developed Using a Synthetic Gene Detects Leptospira-specific Antibodies in Human Serum Samples.

BACKGROUND: Synthetic biology is emerging as a viable alternative for the production of recombinant antigens for diagnostic applications. It offers a safe alternative for the synthesis of antigenic principles derived from organisms that pose a high biological risk. METHODS: Here, we describe an enzyme-linked immunosorbent assay (ELISA) using the synthetic recombinant LipL32 (rLipL32) protein expressed in Escherichia coli for the detection of Leptospira-specific antibodies in human serum samples. The rLipL32-based ELISA was compared with a microscopic agglutination test (MAT), which is currently used as the gold standard for the diagnosis of leptospirosis. RESULTS: Our results showed that all the MAT-positive serum samples were positive for Leptospira-specific IgG in an ELISA, while 65% (n = 13) of these samples were also positive for Leptospira-specific IgM. In the MAT-negative serum samples, 80% and 55% of the samples were detected as negative by an ELISA for Leptospira-specific IgM and IgG, respectively. CONCLUSION: An ELISA using the synthetic rLipL32 antigen was able to distinguish Leptospira-specific IgM (sensitivity 65% and specificity 80%) and IgG (sensitivity 100% and specificity 55%) in human serum samples and has the potential to serve as a rapid diagnostic test for leptospirosis.

Whole genome sequencing of Mycobacterium tuberculosis SB24 isolated from Sabah, Malaysia.

Mycobacterium tuberculosis (M. tuberculosis) is the causative agent of tuberculosis (TB) that causes millions of death every year. We have sequenced the genome of M. tuberculosis isolated from cerebrospinal fluid (CSF) of a patient diagnosed with tuberculous meningitis (TBM). The isolated strain was referred as M. tuberculosis SB24. Genomic DNA of the M. tuberculosis SB24 was extracted and subjected to whole genome sequencing using PacBio platform. The draft genome size of M. tuberculosis SB24 was determined to be 4,452,489 bp with a G + C content of 65.6%. The whole genome shotgun project has been deposited in NCBI SRA under the accession number SRP076503.

Biomarkers of severe dengue disease - a review.

Dengue virus infection presents a wide spectrum of manifestations including asymptomatic condition, dengue fever (DF), or severe forms, such as dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) in affected individuals. The early prediction of severe dengue in patients without any warning signs who may later develop severe DHF is very important to choose appropriate intensive supportive therapy since available vaccines for immunization are yet to be approved. Severe dengue responses include T and B cell activation and apoptosis, cytokine storm, hematologic disorders and complement activation. Cytokines, complement and other unidentified factors may transiently act on the endothelium and alter normal fluid barrier function of the endothelial cells and cause plasma leakage. In this review, the host factors such as activated immune and endothelial cells and their products which can be utilized as biomarkers for severe dengue disease are discussed.

Diagnosis of tuberculous meningitis: challenges and promises.

Tuberculosis (TB) which is caused by Mycobacterium tuberculosis infects primarily the lungs but it also affects other parts of the body. Tuberculous meningitis (TBM) is the most severe form of TB and has the highest mortality and morbidity rate compared to other forms of TB. It is common in young children and HIV-infected patients, but is also seen in adults. Despite anti-tuberculosis treatment, TBM is still a major cause of death and neurological sequelae as treatment given to the patients is often delayed. Early diagnosis is challenging due to the non-specific symptoms of TBM and the low number of tubercle bacilli in cerebrospinal fluid (CSF). Until now, there is no established diagnostic method that can rapidly detect M. tuberculosis in TBM patients with high sensitivity and specificity. The emergence of drug resistant M. tuberculosis strains further complicates the diagnosis and treatment regimen of TBM. This review summarizes challenges of the currently used diagnostic methods and the potential future use of molecular diagnostic methods for TBM.

Expression distribution of cancer stem cells, epithelial to mesenchymal transition, and telomerase activity in breast cancer and their association with clinicopathologic characteristics.

A total of 167 surgically resected primary invasive breast carcinomas and 63 metastatic lymph node lesions were analyzed for immunohistochemical (IHC) localization of the CD44(+)CD24(-low) breast cancer stem cell (CSC) markers, epithelial to mesenchymal transition (EMT) markers, and telomerase activity by double-staining IHC technique, in formalin-fixed, paraffin-embedded tissue, the results were validated by double-staining immunofluorescent and flow cytometry techniques. The results showed that CSCs with CD44(+)CD24(-low) phenotype were significantly increased in node-positive tumors, high-grade tumors, and ductal carcinoma in situ (DCIS). There was a high incidence of telomerase expression in metastatic lymph node lesion. There were considerably high number of tumor cells with EMT expression in metastatic lymph node lesion, and triple-negative tumor. The occurrence of EMT phenomena was usually accompanied by the co-existence of CSCs of CD44(+)CD24(-low) phenotype. There was no association between the existence of CSCs and detection of telomerase activity in tumor cells. Increased numbers of both CSCs of CD44(+)CD24(-low) phenotype and cells underwent EMT in DCIS lesion might be an initial step in the stromal invasion and propagation of breast cancer, and occurrence of EMT in the breast tumor associated with high prevalence of CSCs, promoting tumor invasiveness and metastasis.