“Using long-read sequencing to generate a case-specific reference genome for pathogen strain typing” was the intriguing title of the Oxford Nanopore Community Meeting in Houston I watched tonight. Per Aspera Adastra from Baylor College of Medicine and Texas Children’s Hospital presented. They discussed a case with mother and neonate with Candida infection following fetal surgery leading to preterm birth. Candida parapsilosis was identified and is considered a priority pathogen by the WHO. As part of a retrospective study, physicians wanted to sequence the isolate. Long-read sequencing with R10 flow cells and v14 chemistry, a reference was generated. The sequences were assembled with Flye and polished with Medaka to generate a 13 Mb genome. Next, short-read sequence data was extracted from blood and placental tissue. Average Nucleotide Identity (ANI) suggests the Candida from the neonate and placenta are the same. The team is working on a publication and improving the reference genome. I love the use of sequencing to identify strains and create case-specific reference assemblies.
