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Single Molecule, Real-Time (SMRT) DNA Sequencing Tracks Infectious Disease Pathogens More Effectively Than Short-Read Technologies

Wednesday, September 17, 2014

MENLO PARK, Calif., Sept. 17, 2014 (GLOBE NEWSWIRE) — Pacific Biosciences of California, Inc., (Nasdaq:PACB) provider of the PacBio® RS II DNA Sequencing System, announced the publication of several recent papers highlighting the advantages of Single Molecule, Real-Time (SMRT®) Sequencing over short-read sequencing technologies for infectious disease applications.

Today in Science Translational Medicine1, researchers from the National Institutes of Health, led by senior author Julia Segre, describe how they used SMRT Sequencing to track different bacterial species associated with health-care-associated infections (HAIs) and the spread of antibiotic resistance genes. Of particular concern, the authors note, is the fact that transfer of plasmids (small mobile pieces of DNA) between bacterial species is spreading resistance to a powerful class of antibiotics of last resort called carbapenems, making these HAIs nearly impossible to treat.

Carbapenem-resistant Enterobacteriaceae (CRE) are associated with a 40%-80% mortality rate from infection according to published studies. Further, the incidence of CRE in the US has quadrupled over the past decade and has been found in nearly every state, including nearly 20% of long-term acute care facilities housing some of the most vulnerable patients. “In the face of a dwindling selection of drugs to fight healthcare-associated infections, prevention is critical. 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,” the authors write.

After an outbreak in the NIH Clinical Center in 2011, NHGRI researchers sought to survey and better understand the issue of plasmid “trafficking” in the hospital setting where the environment, patients, and healthcare personnel may each serve as reservoirs. The researchers used SMRT Sequencing to identify and track plasmids within bacterial isolates, revealing a complex pattern of introduction and environmental spread of carbapenemase-encoding plasmids.

Because plasmid sequences contain complexities such as repeats and mobile genetic elements, previous attempts to sequence them with short-read technology were not able to discriminate and resolve plasmid from chromosomal genes. The highly accurate, fully contiguous genome sequence data provided by SMRT Sequencing, including full plasmid identification, challenge previous assumptions about horizontal gene transfer events within patients and point to the possibility of environmental connections.

The results have great implications for allocation of hospital infection control resources. “Given the limited resources in all health care facilities, sequence data can help focus and direct the use of allotted funds for infection control interventions, thus providing the best patient care,” the researchers concluded.

Today’s paper follows several other papers describing the benefits of SMRT Sequencing for infectious disease applications. In one report2, researchers from the University of Pittsburgh and University of Maryland used SMRT Sequencing to generate a complete genome assembly of a Klebsiella pneumoniae strain harboring two different carbapenemase genes. The authors noted that the approach provided fully assembled genome sequences cost-effectively without the need for gap-filling procedures, and was particularly useful in elucidating the complex structures of the large multidrug resistance plasmids.

In another study3, University of Zurich and University College Dublin researchers published the discovery of a new plasmid-harboring antibiotic resistance genes from a K. pneumoniae strain isolated from surface water, suggesting a cause for increased concern about the threat of these pathogens not just in the healthcare setting but in other environments, as well.

In a report4 published earlier this month, researchers from Griffith University in Australia reported how they used SMRT Sequencing to better understand the mechanisms of pathogenicity in Moraxella catarrhalis, a Gram-negative respiratory tract bacteria associated with exacerbations of chronic obstructive pulmonary disease and childhood ear infections. The Griffith University researchers took advantage of the unique capability of SMRT Sequencing to detect and functionally characterize DNA base modifications suspected to be associated with mechanisms of
transmission and/or ability to cause disease in M. catarrhalis-based infections. SMRT technology is the only sequencing technology available that offers detection of base modications as part of the sequencing process.

“SMRT Sequencing has emerged as the gold standard in microbial sequencing for its ability to close genomes into a single contig, resolve plasmids, and detect base modifications such as methylation,” said Jonas Korlach, Chief Scientific Officer of Pacific Biosciences. “Scientists researching infectious diseases recognize that the PacBio RS II is the ideal technology platform for this application, providing the most cost-effective way to get a complete genomic picture of these important disease pathogens.”

Non-microbial infectious disease research has benefited from SMRT Sequencing, as well. A recent paper5 from researchers at the University of Maryland School of Medicine and the National Institute of Allergy and Infectious Diseases reported the most complete genome of a filarial nematode, which was produced by SMRT Sequencing. Filarial nematodes represent a risk to ~20% of the global population, with &#62 180 million individuals already infected.

References:

1Conlan et al. (2014) Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Science Translational Medicine 6: 254ra126.

2Doi et al. (2014) Whole genome assembly of Klebsiella pneumoniae co-producing NDM-1 and OXA-232 carbapenemases using Single-Molecule, Real-Time Sequencing. Antimicrobial Agents and Chemotherapy doi: 10.1128/AAC.03180-14.

3Katrin et al. (2014) A novel Tn3-like composite transposon harboring blaVIM-1 in Klebsiella pneumoniae spp. pneumoniae isolated from river water. Microbial Drug Resistance doi: 10.1089/mdr.2014.0055.

4Blakeway et al. (2014) ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media. FASEB Journal doi: 10.1096/fj.14-256578.

5Tallon et al. (2014) Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis. BMC Genomics 15: 788.

About the PacBio RS II and SMRT Sequencing

Pacific Biosciences’ SMRT Sequencing technology achieves the industry’s longest read lengths, highest consensus accuracy and the least degree of bias. These characteristics, combined with the ability to detect many types of DNA base modifications (e.g., methylation) as part of the sequencing process, make the PacBio RS II an essential tool for many scientists studying genetic and genomic variation. The PacBio platform provides a sequencing solution that can address a growing number of complex medical, agricultural and industrial problems.

About Pacific Biosciences      

Pacific Biosciences of California, Inc. (Nasdaq:PACB) offers the PacBio RS II DNA Sequencing System to help scientists solve genetically complex problems. Based on its novel Single Molecule, Real-Time (SMRT) technology, the company’s products enable: targeted sequencing to more comprehensively characterize genetic variations; de novo genome assembly to more fully identify, annotate and decipher genomic structures; and DNA base modification identification to help characterize epigenetic regulation and DNA damage. By providing access to information that was previously inaccessible, Pacific Biosciences enables scientists to increase their understanding of biological systems. More information is available at www.pacb.com

CONTACT: For Pacific Biosciences:



         Media:

         Nicole Litchfield

         415.793.6468

         nicole@bioscribe.com



         Investors:

         Trevin Rard

         650.521.8450

         ir@pacificbiosciences.com

Source: Pacific Biosciences of California, Inc.

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