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This Week in Genome Research: Apr 17, 2013

An international team led by investigators with the Wellcome Trust Sanger Institute's pathogen genomics group describes a strategy for sequencing the genomes of Chlamydia trachomatis isolates nabbed from clinical swabs without a separate bacterial culturing step. As they report in the early, online edition of Genome Research, the researchers relied on multiple displacement amplification, or MDA, to up the levels of DNA in clinical samples after enriching for the sexually transmitted bugs using a so-called immunomagnetic separation method. Combining the amplification and enrichment techniques helped to sequence the genomes of a significant subset of C. trachomatis specimens found in clinical and archived samples, the team reports, providing "new avenues of investigation for genomic research into difficult-to-culture and fastidious bacteria."

Meanwhile, researchers from the J. Craig Venter Institute and elsewhere explain how they used single-cell sequencing to characterize the genomes of Porphyromonas gingivalis pathogens from the sink drain of a hospital bathroom. That team came up with an automated approach for performing MDA on hundreds of individual bacterial cells in parallel, producing amplified DNA that was then tested by 16S ribosomal RNA sequencing to characterize the microbes present. From there, investigators narrowed in on sequence data for the periodontal disease culprit P. gingivalis, using single-cell sequence assembly software to put an almost complete P. gingivalis genome — a sequence that researchers subsequently compared with existing P. gingivalis genomes.

EMBL's Peer Bork and colleagues used metagenomic sequencing to look at ways in which antibiotic use in food and medicine influences the resistance genes found in microbial communities in the human gut. Using metagenomic sequence data on more than 250 fecal samples from 207 individuals in three countries, the team searched for sequences implicated in resistance to dozens of antibiotic types. Results of the "resistome" analysis indicated that resistance gene representation tends to coincide with the suite of antibiotics that have been long present and/or currently used in agricultural animals in each area.

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.