December 5, 2017  |  General

The antibiotic arms race: Tracking K. pneumoniae in a hospital setting

Courtesy of NIAID

In a recent paper, scientists in Germany call for a genomic database of Klebsiella pneumoniae strains to accelerate strain identification as well as drug-resistance status. To that end, they used SMRT Sequencing to generate high-quality assemblies for 16 isolates collected in German hospitals.

Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing” comes from lead authors Andreas Zautner and Boyke Bunk, senior authors Jorg Overmann and Wolfgang Bohne, and collaborators at University Medical Center and other institutes in Germany.

The urgency to characterize K. pneumoniae strains comes from the rapid rise of carbapenem-resistant Klebsiella given that drug resistance, and increasingly multidrug resistance (MDR), is a major public health threat with these infections. “A continuous monitoring of [strain type] distribution and its association with resistance and virulence genes is essential for early detection of successful K. pneumoniae lineages,” the scientists report.

K. pneumoniae strains carry plasmids encoding different types of carbapenemase, which confers resistance to the carbapenem class of antibiotics. OXA-48 is currently the most common carbapenemase found in K. pneumoniae isolates in Germany, according to the authors; similar strains are commonly found in North Africa, the Middle East, and European countries along the Mediterranean. The team chose to focus on OXA-48 strains, selecting 16 isolates collected in 2013 and 2014 for whole genome SMRT Sequencing.

The technology choice was no accident. “A comprehensive K. pneumoniae database of closed genomes is necessary for a complete understanding of the genome plasticity of these organisms and can significantly improve the tracking of MDR isolates,” the scientists write. With SMRT Sequencing, they were able to generate closed genomes. In most cases they used a single SMRT Cell per strain, and “a consensus concordance of QV60 could be confirmed for all genomes,” they report.
Based on the 16 genome assemblies, the scientists determined that half of the isolates shared the same type, ST147, and differed by no more than 25 SNPs throughout the core genome. They identified several plasmids, including a novel linear plasmid prophage of Klebsiella oxytoca. “The comparative whole-genome analysis revealed several rearrangements of mobile genetic elements and losses of chromosomal and plasmidic regions in the ST147 isolates,” they write.

“Single molecule real-time sequencing allowed monitoring of the genetic and epigenetic microevolution of MDR OXA-48-producing K. pneumoniae,” the team concludes, noting that the approach was amenable to spotting individual SNPs, as well as complex rearrangements.

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