Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA

Sarah Shrum Davis^{1

2

3}, Paris Salazar-Hamm^{3

4

5

6}, Karen Edge¹, Tim Hanosh¹, Jessica Houston¹, Anastacia Griego-Fisher⁷, Francelli Lugo⁸, Nicholas Wenzel⁷, D'Eldra Malone⁷, Carol Bradford⁹, Kelly Plymesser^{1

2}, Michael Baker^{1

2}, Kurt Schwalm¹⁰, Sarah Lathrop², Chad Smelser¹, Darrell L Dinwiddie^{4

10}, Daryl Domman^{11

12

13}

Affiliations

¹ Infectious Disease Epidemiology Bureau, New Mexico Department of Health, Santa Fe, NM, USA.
² University of New Mexico Emerging Infections Program, Office for Community Health, Albuquerque, NM, USA.
³ Biology Department, University of New Mexico, Albuquerque, NM, USA.
⁴ Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
⁵ Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA.
⁶ Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
⁷ Scientific Laboratory Division, New Mexico Department of Health, Albuquerque, NM, USA.
⁸ City of Albuquerque Environmental Health, Albuquerque, NM, USA.
⁹ City of Albuquerque BioPark, Albuquerque, NM, USA.
¹⁰ Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
¹¹ Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA. ddomman@lanl.gov.
¹² Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA. ddomman@lanl.gov.
¹³ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA. ddomman@lanl.gov.

PMID: 40393962
PMCID: PMC12092818
DOI: 10.1038/s41467-025-59766-3

Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA

Sarah Shrum Davis et al. Nat Commun. 2025.

. 2025 May 20;16(1):4680.

doi: 10.1038/s41467-025-59766-3.

Authors

Affiliations

¹ Infectious Disease Epidemiology Bureau, New Mexico Department of Health, Santa Fe, NM, USA.
² University of New Mexico Emerging Infections Program, Office for Community Health, Albuquerque, NM, USA.
³ Biology Department, University of New Mexico, Albuquerque, NM, USA.
⁴ Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
⁵ Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA.
⁶ Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
⁷ Scientific Laboratory Division, New Mexico Department of Health, Albuquerque, NM, USA.
⁸ City of Albuquerque Environmental Health, Albuquerque, NM, USA.
⁹ City of Albuquerque BioPark, Albuquerque, NM, USA.
¹⁰ Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
¹¹ Clinical and Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA. ddomman@lanl.gov.
¹² Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, USA. ddomman@lanl.gov.
¹³ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA. ddomman@lanl.gov.

PMID: 40393962
PMCID: PMC12092818
DOI: 10.1038/s41467-025-59766-3

Abstract

Shigellosis is a gastrointestinal infection caused by species of Shigella. A large outbreak of Shigella flexneri serotype 2a occurred in Albuquerque, New Mexico between May 2021 and November 2023 that involved humans and non-human primates (NHP) from a local zoo. We analyzed the genomes of 202 New Mexican 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 but then predominantly affected people experiencing homelessness. 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. All isolates were multidrug-resistant, including towards fluoroquinolones, a first line treatment option which led to treatment failures in human and NHP populations. We show the circulation of the same S. flexneri strain in humans and NHPs, causing fatalities in both populations. This study demonstrates the threat of antimicrobial resistant organisms to vulnerable human and NHP populations and emphasizes the value of genomic surveillance within a One Health framework.

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Conflict of interest statement

Competing interests: After the manuscript had entered peer‑review, D.L.D. accepted a position at Illumina; this new employment commenced after all data collection and primary analyses were completed and did not influence the study design, interpretation of results, or the preparation of this manuscript. The remaining authors declare no competing interests.

Figures

**Fig. 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 demographic status: daycare, men who have sex with men, (MSM), non-human primate (NHP), out of state, person experiencing homelessness (PEH), PEH-adjacent, and sporadic.

**Fig. 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 non-human 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 five 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.

**Fig. 3. Maximum likelihood phylogeny of *S. flexneri* 2a 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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Update of

Multidrug-resistant Shigella flexneri outbreak associated with a high-mortality spillover event into nonhuman primates.
Domman D, Davis SS, Salazar-Hamm P, Edge K, Hanosh T, Houston J, Griego-Fisher A, Lugo F, Wenzel N, Malone D, Bradford C, Plymesser K, Baker M, Schwalm K, Lathrop S, Smelser C, Dinwiddie D. Domman D, et al. Res Sq [Preprint]. 2024 Jul 12:rs.3.rs-4682172. doi: 10.21203/rs.3.rs-4682172/v1. Res Sq. 2024. Update in: Nat Commun. 2025 May 20;16(1):4680. doi: 10.1038/s41467-025-59766-3. PMID: 39041026 Free PMC article. Updated. Preprint.

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Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA

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Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA

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