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[Preprint]. 2024 Jul 12:rs.3.rs-4682172.
doi: 10.21203/rs.3.rs-4682172/v1.

Multidrug-resistant Shigella flexneri outbreak associated with a high-mortality spillover event into nonhuman primates

Daryl Domman  1 , Sarah Shrum Davis  2 , Paris Salazar-Hamm  3 , Karen Edge  4 , Tim Hanosh  4 , Jessica Houston  4 , Anastacia Griego-Fisher  4 , Francelli Lugo  5 , Nicholas Wenzel  4 , D'Eldra Malone  4 , Carol Bradford  6 , Kelly Plymesser  2 , Michael Baker  2 , Kurt Schwalm  1 , Sarah Lathrop  2 , Chad Smelser  4 , Darrell Dinwiddie  1
Affiliations

Multidrug-resistant Shigella flexneri outbreak associated with a high-mortality spillover event into nonhuman primates

Daryl Domman et al. Res Sq. .

Update in

Abstract

Shigellosis is a gastrointestinal infection caused by species of Shigella. A large outbreak of Shigella flexneri serotype 2a occurred in Albuquerque, New Mexico (NM) between May 2021 and November 2023 that involved humans and nonhuman primates (NHP) from a local zoo. We analyzed the genomes of 202 New Mexico isolates as well as 15 closely related isolates from other states, and four from NHP. The outbreak was initially detected within men who have sex with men (MSM) but then predominantly affected people experiencing homelessness (PEH). Nearly 70% of cases were hospitalized and there was one human death. The outbreak extended into Albuquerque's BioPark Zoo, causing high morbidity and six deaths in NHPs. The NHP isolates were identical to those in the human outbreak. All isolates were multidrug-resistant, including towards fluoroquinolones, a first line treatment option which led to treatment failures in human and NHP populations. We demonstrate the transmission of this S. flexneri strain between humans and NHPs, causing fatalities in both populations. This study demonstrates the threat of antimicrobial resistant organisms to vulnerable human and primate populations and emphasizes the value of vigilant genomic surveillance within a One Health framework.

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Figures

Figure 1:
Figure 1:. Epidemiological curve of a S. flexneri outbreak centered in Bernalillo County, New Mexico.
Cases span from 2019 to 2023 and are colored according to status.
Figure 2:
Figure 2:. Outbreak strain phylogenies and transmission.
A. Time-scaled BEAST phylogeny of outbreak strains. The outbreak clade includes 221 isolates, 202 residents of New Mexico, 15 out of state residents, and 4 nonhuman primates. Nodes are colored by demographic status. The presence of AMR genes are indicated and clustered by drug class. B. Minimum spanning tree of outbreak strains. The nodes are collapsed at 5 SNPs and the size of the circles are proportional to the number of strains within a given node. Nodes are colored by demographic status. Branch lengths correspond to the number of SNPs. C. Transmission inference from BEAST. The size of the circles denotes the number of cases and lines between locations indicate inferred transmission events.
Figure 3:
Figure 3:. Maximum likelihood phylogeny of S. flexneri2a strains related to the New Mexico outbreak circulating within the U.S.
We selected 23 representative sequences from the New Mexico outbreak (red box) and placed these in the context of 105 S. flexneri 2a strains that were less than 65 SNPs to the outbreak strain. Nodes are colored by U.S. state. The presence of AMR genes are indicated and clustered by drug class.
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