Samuel Shelburne from the University of Texas MD Anderson Cancer Center presented at the Nanopore Community Meeting in Boston. The session’s title was “Use of Oxford Nanopore sequencing to evaluate potential transmission of hospital infections.” Shelburne began by discussing healthcare-associated infections (HAIs), which are among the top ten leading causes of death in the US! Infection Prevention and Control is necessary, and infection tracing is complex. Baseline rates of infection are monitored, and clusters of infections are monitored. Shelburne spoke about “cryptic transmission” detected through sequencing studies. They shared data on the transmission of the same strains over several years! In studies in the US and Australia, the time from isolate to sequence analysis was about seventy days. Shelburne described how the project began with a fellow proposing the project and use of Oxford Nanopore Sequencing (ONT) and sequencing about ten isolates a week. Then, the graduate student and Shelburne analyze genetic relatedness and transmission. The project went over twenty-six weeks, and 494 isolates were screened. Half of the isolates (242, 98%) met their criteria. They used the Rapid Barcoding kit and Flyest to assemble. The average depth was ~80. Isolates were sequenced 24 hours, washed, and used again two or three times. Nanopore errors were confirmed with Illumina sequencing. They began base calling with Guppy and moved to Dorado, improving the average Q score from 50 to 60. Forty x coverage was enough to remove (virtually) all errors. They assessed HAI transmission using seqsphere+ and core genome MLST (cgMLST). Antimicrobial resistance genes (AMR) and pathogen epidemiology were analyzed. They had 242 isolates from 218 patients. The graduate student and Shelburne plotted isolates that had epidemiologic links by sharing a ward. I am impressed with their turnaround of about twenty-two strains per week. The team now wants to create an “on-demand platform” for analysis.
