Stand-alone sequencing identifies hospital pathogen transmission clusters
Key takeaways:
- Researchers assessed the Oxford Nanopore Technologies sequencing approach for determining the health care transmission of bacterial pathogens.
- They determined it was accurate, efficient and cost effective.
A stand-alone sequencing approach was accurate, cost effective and efficient for analyzing resistant pathogens and determining their health care-associated transmission, researchers found.
“We wanted to determine whether we could use the [Oxford Nanopore Technologies (ONT)] sequencing approach to assess potential health care transmission of bacterial pathogens,” Samuel Shelburne MD, PhD, professor in the department of infectious diseases, infection control and employee health, and the department of genomic medicine at the University of Texas MD Anderson Cancer Center, told Healio.
“ONT is easier to perform and scale than the current sequencing approach used to assess such transmission,” he said.
Shelburne and colleagues prospectively performed whole-genome sequencing on pathogens with an increased risk of health care transmission using the ONT MinION sequencing device and Dorado base calling algorithm.
The researchers screened electronic health records twice each week to identify bacteria of interest from patients hospitalized for 48 hours or longer at the time of infection onset or from patients with recent contact with the University of Texas MD Anderson Cancer Center within the last 30 days of infection.
A total of 242 bacterial isolates from 216 patients over a 6-month period were assessed, including MRSA, vancomycin-resistant Enterococcus faecium, Pseudomonas aeruginosa, Escherichia coli and Klebsiella pneumoniae, among other species.
According to the study, to identify strains with genetic similarity — which could indicate potential transmission — two-step screening was conducted using Ridom SeqSphereþ for core genome multilocus sequence typing and MINTyper for reference-based core genome single nucleotide polymorphisms using previously published cutoff values.
The accuracy of ONT was assessed against Illumina, which researchers referred to as the “gold standard.”
Overall, the researchers found that the ONT process was “highly accurate.” Specific data from the study showed that after ONT sequencing and parallel Illumina sequencing were performed, ONT achieved a mean identity score of Q60 for assembled genomes, even with a low coverage rate.
Using ONT, the researchers identified 21 isolates that met the criteria for possible transmission. These isolates formed five genetically related clusters, with more than 70% of the cluster isolates originating from patients with links to health care transmission.
The researchers determined the ONT process provided timely data, cost efficiently. Data showed that an average of 10 strains were sequenced per week throughout the study, with the average duration from initiating gDNA extraction to analysis completion being 2 days. The total cost per isolate was estimated to be approximately $250 including labor and $45 without labor.
Based on these data, Shelburne concluded “ONT sequencing might be incorporated into infection control initiatives to try to establish and ultimately prevent transmission of health care pathogens.”
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