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Poultry may be an important source of foodborne, antimicrobial-resistant bacteria to consumers in settings with limited water, sanitation, and hygiene infrastructure. The Chicken Exposures and Enteric Pathogens in Children Exposed through Environmental Pathways (ChEEP ChEEP) study was conducted in Maputo City, Mozambique from 2019 to 2021 to quantify enteric pathogen exposures along the supply chain for commercial and local (i.e., scavenger) chicken breeds. Here, we performed metagenomic sequencing of total DNA from banked ChEEP ChEEP samples to characterize fecal and carcass microbiomes and resistome diversity between chicken breeds and along the supply chain. Fecal samples (\n              <jats:italic>n<\/jats:italic>\n              = 26) were collected from commercial and local chickens at production sites and markets and carcass (\n              <jats:italic>n<\/jats:italic>\n              = 49) and rinse bucket samples (\n              <jats:italic>n<\/jats:italic>\n              = 26) from markets. We conducted taxonomic profiling and identified antimicrobial resistance genes (ARGs) from metagenomic sequence data, focusing especially on potential human pathogens and \u201chigh-risk\u201d ARGs. We estimated alpha diversity for each sample and compared by site and breed. We estimated Bray\u2013Curtis dissimilarity between samples and examined clustering. We found that commercial and local chickens harbored distinct fecal potential pathogens and resistomes at production and market sites. Many potentially pathogenic bacteria and ARGs present in chicken fecal samples are also present on carcasses sold to consumers. Finally, commercial chicken carcasses contain high-risk ARGs that are not necessarily introduced from chicken feces. These results indicate markets are an important site of exposure to potentially pathogenic bacteria and high-risk ARGs.\n            <\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>While chicken eggs and meat are a critical protein source in low-income settings, antibiotics are routinely fed to chickens with consequences for selection of antimicrobial resistance. Evaluating how poultry gut bacterial communities, including potential human pathogens and high-risk antimicrobial resistance genes, differ from farm to market could help identify where to target interventions to minimize transmission risks to human populations. In this study in Maputo City, Mozambique, we found compositional differences between commercial and local chicken breeds at production and market sites. We also found that while all potentially pathogenic bacteria and many high-risk antimicrobial resistance genes persisted from production and market through processing, some resistance genes were detected on carcass samples only after processing, suggesting human or environmental contamination is occurring within markets. Overall, our findings indicate that open-air markets may represent a critical juncture for human exposures to pathogens and antimicrobial resistance genes from poultry and poultry products.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/msystems.01037-24","type":"journal-article","created":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T14:00:25Z","timestamp":1734616825000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Farm-to-fork changes in poultry microbiomes and resistomes in Maputo City, Mozambique"],"prefix":"10.1128","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2175-4138","authenticated-orcid":false,"given":"Natalie","family":"Olson","sequence":"first","affiliation":[{"name":"Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University","place":["Atlanta, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3116-6727","authenticated-orcid":false,"given":"Frederica","family":"Lamar","sequence":"additional","affiliation":[{"name":"Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University","place":["Atlanta, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3110-8343","authenticated-orcid":false,"given":"Herm\u00f3genes","family":"Mucache","sequence":"additional","affiliation":[{"name":"Veterinary Faculty, Universidade Eduardo Mondlane","place":["Maputo, Mozambique"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9038-5922","authenticated-orcid":false,"given":"Jos\u00e9","family":"Fafetine","sequence":"additional","affiliation":[{"name":"Veterinary Faculty, Universidade Eduardo Mondlane","place":["Maputo, Mozambique"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joaquim","family":"Sa\u00edde","sequence":"additional","affiliation":[{"name":"Biotechnology Center, Universidade Eduardo Mondlane","place":["Maputo, Mozambique"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3546-5305","authenticated-orcid":false,"given":"Am\u00e9lia","family":"Milisse","sequence":"additional","affiliation":[{"name":"Biotechnology Center, Universidade Eduardo Mondlane","place":["Maputo, Mozambique"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8914-8631","authenticated-orcid":false,"given":"Denise R. A.","family":"Brito","sequence":"additional","affiliation":[{"name":"Biotechnology Center, Universidade Eduardo Mondlane","place":["Maputo, Mozambique"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4074-3170","authenticated-orcid":false,"given":"Kelsey J.","family":"Jesser","sequence":"additional","affiliation":[{"name":"Department of Environmental and Occupational Health Sciences, University of Washington","place":["Seattle, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0968-9401","authenticated-orcid":false,"given":"Karen","family":"Levy","sequence":"additional","affiliation":[{"name":"Department of Environmental and Occupational Health Sciences, University of Washington","place":["Seattle, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1517-2572","authenticated-orcid":false,"given":"Matthew C.","family":"Freeman","sequence":"additional","affiliation":[{"name":"Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University","place":["Atlanta, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6526-116X","authenticated-orcid":true,"given":"Maya L.","family":"Nadimpalli","sequence":"additional","affiliation":[{"name":"Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University","place":["Atlanta, USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1080\/00439339.2022.2092437"},{"key":"e_1_3_5_3_2","unstructured":"Grace D Makita K Bonfoh B. 2010. 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