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In Acinetobacter Study, Long Reads Aid in Defining Genomic Structure

Monday, March 3, 2014

A paper recently published in mBio, an open access journal from the American Society for Microbiology, reports on the sequencing and phylogenetic analysis of several drug-resistant strains of a pathogen found in hospitals. According to the authors, incorporating PacBio® sequence was critical for generating extremely long contigs for assembly and for accurately identifying chromosomal position and structure of genomic features associated with drug resistance.

The publication, entitled “New Insights into Dissemination and Variation of the Health Care-Associated Pathogen Acinetobacter baumannii from Genomic Analysis,” from scientists at the J. Craig Venter Institute, as well as Case Western Reserve University and its affiliated hospitals. Lead author Meredith Wright, senior author Mark Adams, and their collaborators describe a study of 49 drug-resistant isolates of the A. baumannii nosocomial pathogen gathered during a single year from three branches of a hospital system in Cleveland, Ohio. Their goal was to use sequence information to determine the transmission paths of the organism during that year.

A. baumannii has only become a serious pathogen in the last few decades, and “is now a leading cause of ventilator-associated pneumonia and surgical and urinary tract infections, among other illnesses,” the authors write. That surge in infections is due largely to A. baumannii’s ability to rapidly develop resistance to drugs. With this study, scientists hoped to learn more about that ability, as well as how to prevent disease transmission.

For a deeper understanding of this, two distinct strains were sequenced using Single Molecule, Real-Time (SMRT®) Sequencing and assembled with HGAP.  The PacBio assemblies yielded contig N50 values larger than 1 Mb, compared to about 100 kb for Illumina® assemblies.The authors note that the quality of PacBio-only assemblies was comparable to that of error-corrected hybrid assemblies using Illumina data.

The long reads were particularly important for evaluating the pathogen’s drug-resistance properties, which have been linked to chromosomal and plasmid-borne resistance genes, as well as resistance islands. Because they were able to resolve these elements, the authors write, SMRT Sequencing “aided in defining the genetic structure and chromosomal position of resistance islands” in the two strains.

With this and the rest of the study information, the scientists determined that transmission was not as simple as patient-to-patient. “There was limited spatial or temporal clustering of strain types and gene contents within different hospital components, indicating that an endemic and interacting A. baumannii population exists either within the UH hospital system or in patients colonized with the bacteria,” the authors write. “The movement of patients and staff between the affiliated hospital locations may contribute to strain mixing and diversification.”

Building on that, the scientists note that all of these divergent strains were “indistinguishable by conventional sequence typing methods” and that genomic analysis will be essential for accurately identifying individual strains and determining drug resistance profiles.

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