Sequencing pathogen samples during a communicable disease outbreak is becoming an increasingly common procedure in epidemiologic investigations. Identifying who infected whom sheds considerable light on transmission patterns, high-risk settings and subpopulations, and the effectiveness of infection control. Genomic data shed new light on transmission dynamics and can be used to identify cluster...

Trillions of bacteria, fungi, viruses, archaea, and small arthropods colonize the skin surface, collectively comprising the skin microbiome. Generations of researchers have classified these microbes as transient versus resident, beneficial versus pathogenic, and collaborators versus adversaries. Culturing and direct sequencing of microbial inhabitants identified distinct populations present at ...

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a 'traditional' Sanger sequencing method with two NGS approaches ...

Background and Aims: lamivudine is amongst the antiviral for drug chronic hepatitis B treatment. During therapy with lamivudine, variants may emerge with YMDD mutation in the reverse transcriptase (RT) region of polymerase gene. This mutation might have a role in drug resistant for HBV. Materials and Methods: HBV DNA extraction from serum sample of 88 patients, were subjected to nested PCR for ...

background and aims: lamivudine is amongst the antiviral for drug chronic hepatitis b treatment. during therapy with lamivudine, variants may emerge with ymdd mutation in the reverse transcriptase (rt) region of polymerase gene. this mutation might have a role in drug resistant for hbv. materials and methods: hbv dna extraction from serum sample of 88 patients, were subjected to nested pcr for ...

We characterized the bacterial community from an AMD tailings pond using both classical culturing and modern direct sequencing techniques and compared the two methods. Acid mine drainage (AMD) is produced by the environmental and microbial oxidation of minerals dissolved from mining waste. Surprisingly, we know little about the microbial communities associated with AMD, despite the fundamental ...

The direction of production for indigenous chicken breeds is currently unknown and this knowledge, combined with the development of chicken genome-wide association studies, led us to investigate differences in specific loci between broiler and layer chicken using bioinformatic methods. In addition, we analyzed the distribution of these seven identified loci in four Chinese indigenous chicken br...

A protocol for direct sequencing of polymerase chain reaction (PCR) products from mycelia of Discula umbrinella, a fungal endophyte, using bufferless electrophoresis is described. This improved method allows researchers to conduct high-capacity screening of multiple gene regions for fungal endophytes applicable to microbial ecology and population genetic studies.