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Leishmaniasis is a rare disease in the United States, with an estimated annual incidence of dozens of cases occurring primarily in travelers, migrants, and military personnel. True disease incidence is unknown, since leishmaniasis is not a nationally notifiable condition. Here, we describe the results of molecular leishmaniasis over a 1-year interval (September 2021 to August 2022) when our laboratory served as the primary national reference laboratory for molecular diagnosis of civilian leishmaniasis. We tested 218 specimens submitted from 36 states yielding 94/186 (50.5%) positive cases with species or species complex-level identification and 18 novel mini-exon alleles. Most species belonged to subgenusViannia(75.6%) and associated with cutaneous or mucocutaneous disease. Cases were associated with recent travel (18.1%), travel timing unspecified (7.4%), migration (7.4%), remote travel (2.1%), military (1.1%), or unknown history (63.8%). These data illustrate the clinical utility of molecular testing for leishmaniasis and provide unique insight into disease epidemiology.

BackgroundSyphilis incidence continues to increase dramatically in the United States and yet little is known aboutTreponema pallidum(TP) genomic epidemiology within American metropolitan areas.MethodsWe performed whole genome sequencing andtprKdeep sequencing of 28 TP-containing specimens collected mostly from remnant Aptima swabs from 24 individuals from Seattle Sexual Health Clinic during 2021-2022.ResultsAll 12 individuals infected with Nichols lineage strains were MSM, while a specific SS14 cluster (average 0.33 SNPs) included 1 MSW and five women. All TP strains sequenced were azithromycin resistant via 23S rRNA A2058G mutation. Identical TP genomic sequences were found in pharyngeal and rectal swab specimens taken from the same individuals concurrently.tprKsequences were less variable between patient-matched specimens and between epidemiologically-linked clusters. We detected a 528 bp deletion in thetprKdonor site locus, eliminating ninetprKdonor sites, in TP genomes of three individuals with secondary syphilis, associated with diminution of overalltprKsequence diversity.ConclusionsWe developed an end-to-end workflow for public health genomic surveillance of TP from remnant Aptima swab specimens. With its high rate of gene conversion,tprKsequencing may assist in linking cases beyond routine TP genome sequencing. TP strains with deletions intprKdonor sites currently circulate and are associated with diminished antigenic diversity of the TprK putative outer membrane protein.

Genomic analysis of the monkeypox virus outbreak in Washington State using 109 viral genome sequences collected from July-August 2022 shows low overall genetic diversity, multiple introductions into the state with ongoing community transmission, and potential for coinfection of an individual by multiple strains.BiographyDr. Roychoudhury is Acting Instructor and Director of COVID-19 NGS in the Department of Laboratory Medicine and Pathology at the University of Washington and Associate in the Vaccine and Infectious Disease Division at the Fred Hutchinson Cancer Research Center. Her primary research interests are pathogen genomics and mathematical models of viral evolution and host-pathogen interactions.