The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing

IntroductionDiagnosing Mycoplasma faucium poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements.MethodsThis study analyzes the complete genome sequence of M. faucium, obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing.ResultsGenome analysis revealed limited therapeutic options for the M. faucium infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5’-terminally truncated hsdS pseudogenes with overlapping repeats, indicating the potential for forming alternative hsdS variants through recombination.ConclusionThis study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics

View of Grand Rapids

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View of residence in Kalamazoo

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Grand Rapids view

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View of Grand Rapids, Michigan

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View of Fountain in the park from the north, Kalamazoo

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Improving the Quality of Automatic DNA Sequence Assembly using Fluorescent Trace-Data Classifications

Virtually all large-scale sequencing projects use automatic sequence-assembly programs to aid in the determination of DNA sequences. The computer-generated assemblies require substantial hand-editing to transform them into submissions for GenBank. As the size of sequencing projects increases, it becomes essential to improve the quality of the automated assemblies so that this timeconsuming hand-editing may be reduced. Current ABI sequencing technology uses base calls made from fluorescently-labeled DNA fragments run on gels. We present a new representation for the fluorescent trace data associated with individual base calls. This representation can be used before, during, and after fragment assembly to improve the quality of assemblies. We demonstrate one such use -- end-trimming of sub-optimal data -- that results in a significant improvement in the quality of subsequent assemblies. Introduction A fundamental goal of the Human Genome Project is to determine the seque..

Increasing Consensus Accuracy in DNA Fragment Assemblies by Incorporating Fluorescent Trace Representations

We present a new method for determining the consensus sequence in DNA fragment assemblies. The new method, Trace-Evidence, directly incorporates aligned ABI trace information into consensus calculations via our previously described representation, Trace-Data Classifications. The new method extracts and sums evidence indicated by the representation to determine consensus calls. Using the Trace-Evidence method results in automatically produced consensus sequences that are more accurate and less ambiguous than those produced with standard majorityvoting methods. Additionally, these improvements are achieved with less coverage than required by the standard methods -- using Trace-Evidence and a coverage of only three, error rates are as low as those with a coverage of over ten sequences. Introduction Our goal is to improve the quality and efficiency of automatic DNA sequencing (determining the sequence of bases in DNA molecules). One important task in the sequencing process ..