NCM 2023 Houston: Using long-read sequencing to generate a case-specific reference genome for pathogen strain typing

Using genomic data to monitor the spread of current and emerging pathogens or understanding how to treat and prevent infection requires high-quality pathogen genomes. The recent global increase in fungal infections caused by Candida species has brought attention to the emergence of antimicrobial resistance among fungal pathogens, the rise in incidence of invasive non-albicans Candida (iNAC) species, and the increasing burden this brings to the healthcare system. Many fungal genomes contain long repetitive sequences and GC-rich regions, making assembly challenging when relying solely on short-read sequencing platforms. However, long-read sequencing platforms generate sequence reads that can span these problematic regions and enable the assembly of complete and accurate fungal genomes. Here, nanopore sequencing was utilized in de novo genome assembly of a Candida parapsilosis (one of the leading causes of iNAC infection) isolate derived from the blood specimen of a neonate with sepsis. While the mother of the neonate was asymptomatic, we also generated an additional C. parapsilosis genome derived from placental tissue that upheld a previous microscopy finding of candidiasis in formalin-fixed paraffin-embedded tissue. The generation of high-quality genome assemblies using long-read sequencing enabled comparative genomic analyses of two cases of infection by the same iNAC species and provided invaluable feedback to physicians on a complex case of maternal-fetal transmission at Texas Children’s Hospital.