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Wednesday, February 12, 2020

NARMS Scientists Track Antibiotic Resistance in Foodborne Bacteria Using SMRT Sequencing

Launched in 1996, NARMS is a U. S. public health surveillance system that tracks antimicrobial susceptibility of select foodborne enteric bacteria. We hear a lot about the growing crisis of antibiotic resistance in human health, but it turns out this is just the most visible place it appears as it moves through our complex modern environment. For example, when intensive farming is used to feed large urban populations, antibiotic resistance can first emerge on farms and gain access to human communities through the food system.   One of the key groups on the front lines of monitoring antibiotic resistance from farm…

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Monday, October 7, 2019

Keeping a Close Eye on MRSA: Lessons Learned from PacBio Sequencing Surveillance 

Harm van Bakel When MRSA hits your hospital, what do you do?  If you’re located in Europe or other places where infection rates are still relatively low, you can take a seek-and-destroy approach, isolating an affected patient and working out in concentric circles to identify contacts and potential transmissions.  If you’re in New York City, however, the strategy is not so simple. Hospital-associated infections with methicillin-resistant Staphylococcus aureus are endemic in the Big Apple, and this has required a fresh approach to treat and prevent the costly bacterial menace.  At Mount Sinai Hospital, the strategy now involves SMRT Sequencing. Established…

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Tuesday, August 7, 2018

PacBio Sequencing Reveals Food Processing & Pathogenic Strains of Yeast are the Same Species

Candida krusei, a form of yeast that is known to be drug-resistant and able to cause opportunistic infections in humans What’s in a name? Too much, when it comes to the taxology of yeast, it turns out. Scientists from University College of Dublin have found that two distinctly named species of yeast are in fact 99.6% identical at the base pair level, and collinear. In other words, they are the same species. It was a bit of a shock, especially considering one of the yeast species, Pichia kudriavzevii, is commonly used in food production and classified by the US FDA…

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Tuesday, December 12, 2017

Creating an Epigenetic Barcode to Accurately Characterize Microbial Communities

Unraveling the role of the microbiome in human health and environmental samples is an emerging priority in scientific study. But despite the best advances in sequencing technology, identifying the bacteria, fungi, and other organisms present in complex samples remains a huge challenge. Metagenomic shotgun sequencing can read chromosomes, plasmids, and bacteriophages, and comparison to reference genome sequences can be used to place them into putative taxa and species bins, but these methods fail to sufficiently distinguish between genomes that are very similar. A team of scientists from the Icahn School of Medicine at Mount Sinai, Sema4, and other institutions has…

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Tuesday, December 5, 2017

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…

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Friday, March 3, 2017

‘Mobilome’ Study of Antibiotic Resistance Implicates Transposon Activity

Klebsiella pneumoniae A recent effort to understand the genetic mechanisms behind swappable elements of drug-resistance among bacteria built on previous studies of Enterobacteriaceae isolates collected at the National Institutes of Health Clinical Center. The work was made possible by high-quality genome assemblies of these organisms generated earlier with SMRT Sequencing technology. In this project, scientists from the U.S., France, and Brazil teamed up to learn precisely how drug-resistance plasmids are spread from one species to another. They report the results of that investigation in mBio with the publication “Mechanisms of Evolution in High-Consequence Drug Resistance Plasmids” from lead author Susu He,…

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