Genomic Modeling of an Outbreak of Multidrug-Resistant Shigella sonnei, California, USA, 2023-2024

Abstract

We report the detection of a Shigella sonnei outbreak from a small investigation in the San Francisco Bay area, California, USA, in 2024. By combining outbreak investigation with genomic sequencing, we show the utility of phylodynamics to aid outbreak investigations of bacterial pathogens by state or local public health departments.

Keywords: California; Shigella sonnei; United States; antimicrobial resistance; bacteria; epidemiology; multidrug resistance; outbreak; phylodynamic modelling.

Figure 1

Epidemiologic curve showing specimen collection dates of shigellemia cases and housing status in Shigella sonnei case investigation with known linkages, California, USA, 2023–2024.

Figure 2

Diagram showing the number of cases from linked facilities, the housing status of patients, and the linkage between cases in Shigella sonnei case investigation with known linkages, California, USA, 2023–2024.

Figure 3

Maximum clade credibility tree of outbreak samples and contextualized Shigella sonnei isolates from the United States, 2015–2023. The color scale denotes the probability of the node below each branch being in the San Francisco Bay, California, USA, area. Inferred by using MASCOT (6).

Figure 4

Distribution curve of the predicted dates of the most recent common ancestor of the Shigella sonnei outbreak isolates, California, USA, 2023–2024. The plot shows the posterior density for the common ancestor times of the Shigella sequences collected in the San Francisco Bay, California, USA, area. For a single introduction, the common ancestor time provides a lower bound on the timing of the introduction into the San Francisco Bay area.

Figure 5

Phylogenetic tree of Shigella sonnei outbreak isolates in the San Francisco Bay, California, USA, area with spatiotemporal metadata and tree uncertainty, 2023–2024. Branches are colored according to location. The opacity of the branches is equal to the uncertainty of the placement of each branch. Phylodynamic methods are incorporated into phylogenetic trees with time and location.