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NIH Study: Finished Genomes Provide Actionable Data to Combat Spread of Drug-Resistant Bacteria

Wednesday, September 17, 2014

A study launched over concerns around hospital-acquired infections has led to a recommendation for better microbial screening of patients upon admission. The research, from scientists at several NIH institutes, found that cases of hospital-acquired infection were less common than cases where patients were likely already colonized but received false negative results from basic screening.

The study was made possible by Single Molecule, Real-Time (SMRT®) Sequencing, which allowed researchers to sequence plasmids and analyze their diversity and likely phylogeny. Short-read sequencing and strain-typing technologies could not provide the information necessary for a comprehensive analysis.

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae,” published today in Science Translational Medicine, comes from senior author Julie Segre at the National Human Genome Research Institute. In the project, NIH scientists sequenced 20 isolates of carbapenem-resistant Enterobacteriaceae — including two from a Klebsiella pneumonia outbreak at the NIH Clinical Center in 2011, 16 from routine patient and environmental surveillance after the outbreak, and two from former NIH clinic patients found to be positive for the bacteria after being released.

According to the paper, carbapenem-resistant Enterobacteriaceae are a serious concern in healthcare because of their resistance to most or all antibiotics as well as their rapidly increasing incidence — they are now detected four times as often in patients as they were 10 years ago. Because these pathogens carry their drug resistance in plasmids, there is risk that resistance could be acquired by other bacteria. The scientists found it essential to develop a clear view of how these organisms functioned and spread among patients, but quickly determined that short-read sequencers couldn’t provide the whole picture. Plasmids were large — up to 200 kb — and full of repetitive and mobile elements that were intractable with short-read data.

SMRT Sequencing enabled the scientists to analyze and fully assemble all 20 genome sequences for various Enterobacteriaceae with carbapenem resistance. The genomes ranged from 3.9 Mb to 6.2 Mb, with the largest plasmid weighing in at 379 kb. The team independently validated the PacBio® data with optical mapping and short-read sequencing, finding that the accuracy for each genome was better than 99.9999% (Q60). After fully analyzing the genomes, the scientists confirmed that standard approaches such as PCR, multilocus sequence typing, and pulsed-field gel electrophoresis would not have been able to distinguish between certain strains, leaving out valuable information that would have helped track transmission.

Among the paper’s findings, Conlan et al. were able to trace the transmission path of the original carbapenem-resistant Klebsiella outbreak from its index patient to 17 other patients. They also found one patient who was colonized with two different strains of carbapenem-resistant Enterobacteriaceae, and a single patient who acquired the bacteria from another patient while in the hospital. “This case is the only example from the five suspected cases that resulted in a definitive conclusion that nosocomial transmission had occurred, again underscoring the power of genomic sequencing in the clinical setting,” the authors write. They were surprised to find just a few cases of horizontal plasmid transfer, noting instead that “the number of independent introductions observed was surprisingly high and indicated a complex network of plasmids with incredible diversity.” Finally, they identified a new plasmid encoding for carbapenemase that may have significant clinical impact.

“On the basis of our sequence data demonstrating that only 1 of the 10 cases represented nosocomial spread, we directed our resources toward surveillance at admission for carbapenemase-producing organisms,” the researchers report. The clinical team also increased measures aimed at containing bacterial transmission, including taking surveillance cultures from patients more often.

As antibiotic resistance becomes more common and new antibiotics remain rare, it is more important than ever to prevent infection, according to the authors. “In addition to implementing recommended infection control measures such as surveillance, hand hygiene, and barrier precautions, we must find more sophisticated methods to detect, track, and eradicate multidrug-resistant bacteria.”

Whole-genome sequencing is one powerful response that yields actionable medical data, they add. “Sequencing can elucidate the landscape of bacterial transmission, allowing hospitals to target funds and personnel for infection control interventions that provide the best patient care,” they write. “The cost of whole-genome sequencing is dwarfed by [other] costs associated with outbreaks and their investigations, including the human and financial toll and the loss of patient confidence in the health care facility.”

UPDATE: This paper came out at a pivotal time in the fight against antibiotic resistance. Just a day later, the White House issued a report from the President’s Council of Advisors on Science and Technology entitled “Combating Antibiotic Resistance.” At the same time, President Obama issued an executive order calling for the development of a national plan to address this challenge. Check out this blog post for a summary of the efforts.

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PacBio Grants Equity Incentive Award to New Employee

Friday, January 14, 2022