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

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.

Attitudes, practices, and zoonoses awareness of community members involved in the bushmeat trade near Murchison Falls National Park, northern Uganda.

The harvest of bushmeat is widespread in the tropics and sub-tropics. Often in these communities, there is a dependence on bushmeat for both food security and basic income. Despite the importance of bushmeat for households worldwide, the practice raises concern for transmission of zoonotic pathogens through hunting, food preparation, and consumption. In Uganda, harvest of wildlife is illegal, but bushmeat hunting, is commonplace. We interviewed 292 women who cook for their households and 180 self-identified hunters from 21 villages bordering Murchison Falls National Park in Uganda to gain insights into bushmeat preferences, opportunity for zoonotic pathogen transmission, and awareness of common wildlife-associated zoonoses. Both hunters and women who cook considered primates to be the most likely wildlife species to carry diseases humans can catch. Among common zoonotic pathogens, the greatest proportions of women who cook and hunters believed that pathogens causing stomach ache or diarrhea and monkeypox can be transmitted by wildlife. Neither women who cook nor hunters report being frequently injury during cooking, butchering, or hunting, and few report taking precautions while handling bushmeat. The majority of women who cook believe that hunters and dealers never or rarely disguise primate meat as another kind of meat in market, while the majority of hunters report that they usually disguise primate meat as another kind of meat. These data play a crucial role in our understanding of potential for exposure to and infection with zoonotic pathogens in the bushmeat trade. Expanding our knowledge of awareness, perceptions and risks enables us to identify opportunities to mitigate infections and injury risk and promote safe handling practices.