Genomic Epidemiology Linking Nonendemic Coccidioidomycosis to Travel

Abstract

Coccidioidomycosis is a fungal infection endemic to hot, arid regions of the western United States, northern Mexico, and parts of Central and South America. Sporadic cases outside these regions are likely travel-associated; alternatively, an infection could be acquired in as-yet unidentified newly endemic locales. A previous study of cases in nonendemic regions with patient self-reported travel history suggested that infections were acquired during travel to endemic regions. We sequenced 19 Coccidioides isolates from patients with known travel histories from that earlier investigation and performed phylogenetic analysis to identify the locations of potential source populations. Our results show that those isolates were phylogenetically linked to Coccidioides subpopulations naturally occurring in 1 of the reported travel locales, confirming that these cases were likely acquired during travel to endemic regions. Our findings demonstrate that genomic analysis is a useful tool for investigating travel-related coccidioidomycosis.

Keywords: Coccidioides phylogeography; airborne infections; coccidioidomycosis; epidemiology; fungi; genomics; respiratory infections; travel-related illness; whole-genome sequencing.

Figure 1

Summarized maximum-likelihood phylogenetic tree for Coccidioides posadasii isolates from study of genomic epidemiology linking nonendemic coccidioidomycosis to travel and reference isolates. Each recognized phylogeographic clade is highlighted with a colored gradient labeled in its top right corner. Samples with travel history are presented with locations of isolation and all known patient travel, with colors for the geographic regions. Red bold tip labels indicate samples sequenced for this study; other samples are included when including travel history or otherwise mentioned in the main text.

Figure 2

Summarized maximum-likelihood phylogenetic tree for Coccidioides immitis isolates from study of genomic epidemiology linking nonendemic coccidioidomycosis to travel and reference isolates. Each recognized phylogeographic clade is highlighted with a colored gradient labeled in its top right corner. Samples with travel history are presented with locations of isolation and all known patient travel, with colors for the geographic regions. Red bold tip labels indicate samples sequenced for this study; other samples are included when including travel history or otherwise mentioned in the main text.