May 29, 2014  |  General

Research Studies Use Sequencing to Track Path of Infection Outbreaks

A talk at last week’s ASM conference continued the recent trend of scientists using Single Molecule, Real-Time (SMRT®) Sequencing in research projects designed to better understand the transmission path of hospital-acquired infections.

The presentation, entitled “Tracking Hospital Patients and Environment with Complete Genome Sequencing of Carbapenem-Resistant Klebsiella pneumoniae and other Enterobacteriaceae,” came from Julie Segre, a chief investigator at the National Human Genome Research Institute.

Segre spoke of Klebsiella as “the nightmare bug.” From the earliest reports of it in 2001, it is now in more than 40 states in the US and shows strong resistance to antibiotics. The study she presented at ASM was based on patients infected with carbapenem-resistant Klebsiella at the NIH Clinical Center in 2011. The first patient was put in isolation when the bug was identified, but another patient was diagnosed with it five weeks later; in the period that followed, hospital staff identified new patients with the bug as often as once a week for a total of 18 infected patients.

Segre said that the majority of hospital-acquired Klebsiella cases are sequence type 258, which can be identified with a pulse-field technology. This was used to positively diagnose the first four patients, but the tool could not tell whether these patients had infected each other or had acquired the bug independently. For this study, Segre and her team decided that whole-genome sequencing could help them build a phylogeny to recreate the history of these Klebsiella cases and determine how transmission was occurring.

The project was completed using the PacBio® platform because Segre needed to have high-quality genomic and plasmid sequences for the best view of the microbe, which gets its drug-resistance quality from a plasmid. The team studied samples taken from various patients, and even various sites on each patient’s body, and used epidemiology skills to build a transmission map for the outbreak. Based on genome sequence and plasmid diversity, the team determined that there were two separate infection events; some transmission cases from the first patient, and an independent infection in another patient. They also found horizontal gene transfer from patient to environment, highlighting a path that could explain transmission within the hospital.

In her talk, Segre noted that once sequencing technologies are ready for clinical use, they will be essential in stopping this kind of outbreak because they can identify critical infection elements much faster than existing technologies. A recent commentary in Nature shares the perspective, remarking that in the future it will be very important to find ways of rapidly identifying microbes in a hospital setting.

The ASM talk reminded us of a study published earlier this year on analyzing Acinetobacter strains to track infections in several hospitals in Ohio.

Don’t forget, we are hosting our SMRTest Microbe grant program and there’s still time to enter. The winner will receive a sequencing run on the PacBio RS II using one SMRT Cell 8Pac and up to four library constructions. To tell us why your microbial project should be funded, check out the program details and enter here.

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