Genomic reconstruction and directed interventions in a multidrug-resistant Shigellosis outbreak in Seattle, WA, USA: a genomic surveillance study

Abstract

Background: Shigella spp have been associated with community-wide outbreaks in urban settings. We analysed a sustained shigellosis outbreak in Seattle, WA, USA, to understand its origins and mechanisms of antimicrobial resistance, define ongoing transmission patterns, and optimise strategies for treatment and infection control.

Methods: We did a retrospective study of all Shigella isolates identified from stool samples at the clinical laboratories at Harborview Medical Center and University of Washington Medical Center (Seattle, WA, USA) from May 1, 2017, to Feb 28, 2022. We characterised isolates by species identification, phenotypic susceptibility testing, and whole-genome sequencing. Demographic characteristics and clinical outcomes of the patients were retrospectively examined.

Findings: 171 cases of shigellosis were included. 78 (46%) patients were men who have sex with men (MSM), and 88 (52%) were people experiencing homelessness (PEH). Although 84 (51%) isolates were multidrug resistant, 100 (70%) of 143 patients with data on antimicrobial therapy received appropriate empirical therapy. Phylogenomic analysis identified sequential outbreaks of multiple distinct lineages of Shigella flexneri and Shigella sonnei. Discrete clonal lineages (ten in S flexneri and nine in S sonnei) and resistance traits were responsible for infection in different at-risk populations (ie, MSM, PEH), enabling development of effective guidelines for empirical treatment. The most prevalent lineage in Seattle was probably introduced to Washington State via international travel, with subsequent domestic transmission between at-risk groups.

Interpretation: An outbreak in Seattle was driven by parallel emergence of multidrug-resistant strains involving international transmission networks and domestic transmission between at-risk populations. Genomic analysis elucidated not only outbreak origin, but directed optimal approaches to testing, treatment, and public health response. Rapid diagnostics combined with detailed knowledge of local epidemiology can enable high rates of appropriate empirical therapy even in multidrug-resistant infection.

Funding: None.

Figure 1.. Timeline of Shigellosis cases in Seattle, Washington, USA, by demographic group and species.

Vertical axis indicates density of infections sampled in each specified demographic group over time. A parallel timeline showing relative case density normalized by group is presented in Supplemental Figure 1 to better display waves of transmission between at-risk populations, including relatively small but important groups such as such as patients identifying as both MSM and PEH. MSM: men who have sex with men, PEH: persons experiencing homelessness.

Figure 2.. Cladogram showing molecular epidemiology, resistance, and clinical characteristics of S. flexneri isolates.

Relevant metadata are reported circumferentially, followed by isolate identification labels. Lettered arcs around the periphery indicate specific events during procession of the outbreak: A) Serial introduction of phylogenetically distinct S. flexneri strains into Seattle over several decades. In each clade, lineages most closely related to the ancestral node were isolated from MSM. Lineages vary in accessory AMR gene content but are uniformly ciprofloxacin-susceptible. Sharing of AMR genes among unrelated lineages is common, consistent with horizontal gene transfer. B) Detection of a new ciprofloxacin-resistant strain in MSM. C) A new strain is observed at the demographic interface of the MSM/PEH populations (e.g., 190101) and loses resistance to azithromycin and TMP-SMX at the same juncture. D) Strain spreads rapidly through PEH population. E) Emergence of MDR derivatives through combination of chromosomally mediated ciprofloxacin resistance with plasmid-mediated macrolide/TMP-SMX/ceftriaxone resistance. MDR is associated with inappropriate empiric therapy and hospitalization. MSM: men who have sex with men, PEH: persons experiencing homelessness, TMP-SMX: trimethoprim-sulfamethoxazole.

Figure 3.. Annotated timeline of S. flexneri lineage 3 isolates and related references sequences.

Estimated dates of divergence based on time-measured Bayesian analysis of molecular sequences. Phylogenomic and epidemiological links are consistent with international dissemination of this strain from China to Seattle in association with international travel but should not be interpreted to portray case-level transmission events. Tips labeled in grey represent study isolates without demographic risk group information. A simplified version of this tree annotated with 95% highest posterior density intervals is provided as Supplemental Figure 6.

Figure 4.. Cladogram showing molecular epidemiology, resistance, and clinical characteristics of S. sonnei isolates.

Relevant metadata are reported circumferentially, followed by isolate identification labels. Lettered arcs around the periphery indicate specific events during procession of the outbreak: A) Serial introduction of phylogenetically distinct S. sonnei strains over several years. Sharing of resistance plasmids is common among unrelated strains. B) Detection of a new bla_CTX-M-27 extended-spectrum beta-lactamase-carrying strain in the MSM population, 2019. C) This new strain spreads between MSM and PEH populations and loses plasmid-mediated resistance to TMP-SMX at this same juncture. Cases have high rates of inappropriate empiric treatment and hospitalization. D) Strain spreads rapidly through PEH population. E) Recent emergence of multidrug-resistant phenotype in unrelated strain (clade 5) with both pKSR100 and p183660 resistance plasmids. MSM: men who have sex with men, PEH: persons experiencing homelessness, TMP-SMX: trimethoprim-sulfamethoxazole.