Meeting News Coverage

Rapid DNA sequencing device identifies UTI pathogens, resistance

SAN DIEGO — A rapid DNA sequencing device may effectively identify pathogens and antibiotic resistance in patients at high risk for urosepsis, according to a study presented at ICAAC 2015.

Researchers used the novel MinION Nanopore Sequencing device (Oxford Nanopore Technologies), the size of a USB stick, to characterize DNA in 10 urine samples that contained 10⁹ colony-forming units (CFU)/mL of Escherichia coli. The readings were compared with data from the Comprehensive Antibiotic Resistance database.

With the MinION device, E. coli was accurately identified in six samples, according to the researchers. Other pathogens found (Klebsiella pneumoniae and Enterobacter cloacae) also matched with pathogens found through standard culture procedures and were collected within 12 hours.

“This is a quarter of the time needed for conventional microbiology,” Justin O’Grady, PhD, MSc, from the University of East Anglia’s Norwich Medical School, said in a press release. “Swift results like these will make it possible to refine a patient’s treatment much early, and that’s good for the patient, who gets the ‘right’ antibiotic, and for society which can better manage or ‘steward’ its limited supply of antibiotics.”

Poor results from the other four samples may be due to inadequate human DNA depletion, according to the researchers. In addition, the readings were not as precise in characterizing alleles NDM-1, CTX-M-15, TEM-1, and CMY-2. The device also failed to detect quinolone resistance mutations.

Acquired resistance genes that were identified using the device — aacC2, aacC3, aadA2, aadA3, aadA5, aac6’-1b-cr, strAB, blaNDM, blaCTX-M-gp1, blaCMY, blaOXA-31, blaOXA-181, sul1, dfrA1, dfrA12, rmtB, qnrS3, and tetA — corresponded with those identified by Illumina sequencing technology. – by Stephanie Viguers

Reference:

Schmidt K, at al. Abstract D-714. Presented at: Interscience Conference on Antimicrobial Agents and Chemotherapy; Sept. 17-21, 2015; San Diego.

Disclosure: O’Grady reports having a research relationship with Oxford Nanopore Technologies. Please see the abstract for a list of all other authors’ relevant financial disclosures.

SAN DIEGO — A rapid DNA sequencing device may effectively identify pathogens and antibiotic resistance in patients at high risk for urosepsis, according to a study presented at ICAAC 2015.

Researchers used the novel MinION Nanopore Sequencing device (Oxford Nanopore Technologies), the size of a USB stick, to characterize DNA in 10 urine samples that contained 10⁹ colony-forming units (CFU)/mL of Escherichia coli. The readings were compared with data from the Comprehensive Antibiotic Resistance database.

With the MinION device, E. coli was accurately identified in six samples, according to the researchers. Other pathogens found (Klebsiella pneumoniae and Enterobacter cloacae) also matched with pathogens found through standard culture procedures and were collected within 12 hours.

“This is a quarter of the time needed for conventional microbiology,” Justin O’Grady, PhD, MSc, from the University of East Anglia’s Norwich Medical School, said in a press release. “Swift results like these will make it possible to refine a patient’s treatment much early, and that’s good for the patient, who gets the ‘right’ antibiotic, and for society which can better manage or ‘steward’ its limited supply of antibiotics.”

Poor results from the other four samples may be due to inadequate human DNA depletion, according to the researchers. In addition, the readings were not as precise in characterizing alleles NDM-1, CTX-M-15, TEM-1, and CMY-2. The device also failed to detect quinolone resistance mutations.

Acquired resistance genes that were identified using the device — aacC2, aacC3, aadA2, aadA3, aadA5, aac6’-1b-cr, strAB, blaNDM, blaCTX-M-gp1, blaCMY, blaOXA-31, blaOXA-181, sul1, dfrA1, dfrA12, rmtB, qnrS3, and tetA — corresponded with those identified by Illumina sequencing technology. – by Stephanie Viguers

Reference:

Schmidt K, at al. Abstract D-714. Presented at: Interscience Conference on Antimicrobial Agents and Chemotherapy; Sept. 17-21, 2015; San Diego.

Disclosure: O’Grady reports having a research relationship with Oxford Nanopore Technologies. Please see the abstract for a list of all other authors’ relevant financial disclosures.

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