Alda Pires

Title(s)Agronomist, VM: Population Health & Reproduction
SchoolSchool of Veterinary Medicine
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    Title(s)Specialist in Cooperative Extension, ANR VM: Population Health & Reprod

    Title(s)Department Vice Chair, VM: Population Health & Reproduction

    Title(s)Senior Lecturer, VM: Population Health & Reproduction


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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Risk Factors Associated with Generic E. coli Survival in Soils from Certified Organic Farms. J Food Prot. 2026 Aug 05; 100883. Nie K, Cheong S, Baron JN, Jay-Russell MT, Melo Ramos T, Aminabadi P, Millner PD, Kenney A, Hashem F, Pagliari PH, Hutchinson M, Martínez-López B, Bihn EA, Clements DP, Shade JB, Sciligo AR, Pires AFA. PMID: 42556730.
      View in: PubMed   Mentions:    Fields:    
    2. Microbial Food Safety Risk in Finished Soil Amendments: A Statewide Cross-Sectional Study of Organic Waste Processing Systems in California. J Food Prot. 2026 Aug; 89(8):100844. Nie K, McWright L, Rothwell JG, Mondragon-Becerra M, Malal H, Lazcano C, Geisseler D, Scott L, Elliott Campbell J, Gomez-Ortega J, Waterhouse H, Leauthaud A, Duwadi S, Ryals R, Pires AFA. PMID: 42323090.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCellsPHPublic Health
    3. Survival of E. coli TVS353 in Soil Mesocosms at Various Moisture Levels and Light Exposure in Controlled Environments. J Food Prot. 2026 Jun; 89(6):100799. Kapoor HK, Tewari A, Dev Kumar G, Dutta B, Pires AFA, Baur P, Dunn LL, Critzer F, Mishra A. PMID: 42069220.
      View in: PubMed   Mentions:    Fields:    Translation:CellsPHPublic Health
    4. Rethinking navel size thresholds for omphalitis diagnosis in newborn dairy calves using machine learning. JDS Commun. 2026 May; 7(3):378-383. Rico A, Pires AFA, Silva-Del-Rio N. PMID: 42077490; PMCID: PMC13131414.
      View in: PubMed   Mentions:
    5. Genomic characterization of Listeria monocytogenes isolated from small ruminants in integrated crop-livestock systems. BMC Microbiol. 2026 01 06; 26(1):81. Cheong S, Rothwell JG, Schlesener C, Weimer BC, Miramontes C, Pereira RV, Pagliari P, Pires AFA. PMID: 41495644; PMCID: PMC12870440.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCellsPHPublic Health
    6. Risk Factors Associated with Generic Escherichia coli Presence in Fresh Produce Grown in Manure-Amended Soil in Certified Organic Farms. J Food Prot. 2026 02; 89(2):100683. Nie K, Rothwell JG, Baron JN, Jay-Russell MT, Maier G, De Melo Ramos T, Aminabadi P, Haghani V, Millner PD, Kenney A, Hashem F, Pagliari PH, Hutchinson M, Martínez-López B, Bihn EA, Clements DP, Shade JB, Sciligo AR, Pires AFA. PMID: 41419087.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCellsPHPublic Health
    7. Cross-Sectional Study on Zoonotic Bacteria Carriage by Small Ruminants from Portugal's Central Region. Pathogens. 2025 Oct 23; 14(11). Pereira MA, Baptista AL, Cruz R, Esteves F, Amaro A, Mesquita JR, Almeida E, Braguez J, Malva M, Pires AFA. PMID: 41305319; PMCID: PMC12655204.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    8. Temporal and Environmental Drivers for Survival of Escherichia coli in Florida Soils Amended with Heat-Treated Poultry Pellets and Composted Poultry Litter. J Food Prot. 2025 12 10; 88(12):100639. Kapoor HK, Appolon CB, Bardsley CA, Kharel K, Schneider KR, Sharma M, Mishra AK, Dev Kumar G, Pires AFA, Dunn LL, Mishra A. PMID: 41109531.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCellsPHPublic Health
    9. Exploring the impact of grazing on fecal and soil microbiome dynamics in small ruminants in organic crop-livestock integration systems. PLoS One. 2025; 20(1):e0316616. Cheong S, Aguirre-Siliezar K, Williams SR, Gaudin ACM, Pagliari P, Jay-Russell MT, Busch R, Maga EA, Pires AFA. PMID: 39823448; PMCID: PMC11741640.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCellsPHPublic Health
    10. A scoping review of studies reporting biosecurity practices in small and backyard farms raising livestock or poultry in developed countries, 2000-2022. Prev Vet Med. 2025 Mar; 236:106423. Di Francesco J, Isenhower E, Fausak ED, Silva-Del-Rio N, Pires AFA. PMID: 39824150.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    11. Cross-Sectional Study Assessing Management Practices and Udder Health in California Sheep Flocks and Seroprevalence of Small Ruminant Lentivirus. Animals (Basel). 2024 Aug 13; 14(16). Digianantonio R, Pires AFA, Busch R. PMID: 39199866; PMCID: PMC11350894.
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    12. Assessment of the knowledge and behavior of backyard and small-scale producers in California regarding disease prevention, biosecurity practices and antibiotics use. PLoS One. 2022; 17(11):e0277897. Lee K, Pereira RV, Martínez-López B, Busch RC, Pires AFA. PMID: 36409736; PMCID: PMC9678316.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimals
    13. Survey of Management Practices and Farmers' Perceptions of Diseases on Organic Dairy Cattle Farms in California. Animals (Basel). 2022 Sep 21; 12(19). Cheong S, Di Francesco J, Lee K, Van Vleck Pereira R, Black R, Karle B, Lema M, Pires AFA. PMID: 36230266; PMCID: PMC9558946.
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    14. Identification of high-risk contact areas between feral pigs and outdoor-raised pig operations in California: Implications for disease transmission in the wildlife-livestock interface. PLoS One. 2022; 17(6):e0270500. Patterson L, Belkhiria J, Martínez-López B, Pires AFA. PMID: 35763526; PMCID: PMC9239460.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    15. Risk factors of Shiga toxin-producing Escherichia coli in livestock raised on diversified small-scale farms in California. Epidemiol Infect. 2022 06 01; 150:e125. Patterson L, Navarro-Gonzalez N, Jay-Russell MT, Aminabadi P, Pires AFA. PMID: 35641482; PMCID: PMC9274804.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    16. Role of soil in the regulation of human and plant pathogens: soils' contributions to people. Philos Trans R Soc Lond B Biol Sci. 2021 09 27; 376(1834):20200179. Samaddar S, Karp DS, Schmidt R, Devarajan N, McGarvey JA, Pires AFA, Scow K. PMID: 34365819; PMCID: PMC8349628.
      View in: PubMed   Mentions: 23     Fields:    Translation:PHPublic Health
    17. Evaluating the association between climatic factors and sheep condemnations in the United States using cluster analysis and spatio-temporal modeling. Prev Vet Med. 2021 06; 191:105342. O'Hara KC, Pires AFA, Martínez-López B. PMID: 33848741.
      View in: PubMed   Mentions: 1     Fields:    
    18. Detection of Cephalosporin and Fluoroquinolone Resistance Genes via Novel Multiplex qPCR in Fecal Salmonella Isolates From Northern Californian Dairy Cattle, 2002-2016. Front Microbiol. 2021; 12:601924. Basbas C, Byrne BA, Chigerwe M, Escobar ED, Hodzic E, Pires AFA, Pereira RV. PMID: 33658984; PMCID: PMC7917062.
      View in: PubMed   Mentions: 2  
    19. Salmonella and Escherichia coli Prevalence in Meat and Produce Sold at Farmers' Markets in Northern California. J Food Prot. 2020 Nov 01; 83(11):1934-1940. Pires AFA, Stover J, Kukielka E, Haghani V, Aminabadi P, de Melo Ramos T, Jay-Russell MT. PMID: 32502236.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    20. Assessment of veterinarians' engagement with backyard poultry and small-scale livestock operations in four western states. J Am Vet Med Assoc. 2020 Jul 15; 257(2):196-209. Pires AFA, Peterson A, Baron JN, Adams R, Moore DA. PMID: 32597725.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    21. Improving Biosecurity Procedures to Minimize the Risk of Spreading Pathogenic Infections Agents After Carcass Recycling. Front Microbiol. 2020; 11:623. Pandey P, Vidyarthi SK, Vaddella V, Venkitasamy C, Pitesky M, Weimer B, Pires AFA. PMID: 32390969; PMCID: PMC7188909.
      View in: PubMed   Mentions: 5  
    22. Prevalence and risk factors associated with Campylobacter spp. and Salmonella enterica in livestock raised on diversified small-scale farms in California. Epidemiol Infect. 2019 12 12; 147:e321. Pires AFA, Patterson L, Kukielka EA, Aminabadi P, Navarro-Gonzalez N, Jay-Russell MT. PMID: 31826785; PMCID: PMC7006025.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    23. Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California. PeerJ. 2019; 7:e6546. Pereira R, Williams DR, Rossitto P, Adaska J, Okello E, Champagne J, Lehenbauer TW, Li X, Chase J, Nguyen T, Pires AFA, Atwill ER, Aly SS. PMID: 30923650; PMCID: PMC6431540.
      View in: PubMed   Mentions: 9     Fields:    
    24. Small-scale and backyard livestock owners needs assessment in the western United States. PLoS One. 2019; 14(2):e0212372. Pires AFA, Peterson A, Baron JN, Adams R, Martínez-López B, Moore D. PMID: 30763403; PMCID: PMC6375643.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimalsPHPublic Health
    25. Persistence of Escherichia coli in the soil of an organic mixed crop-livestock farm that integrates sheep grazing within vegetable fields. Zoonoses Public Health. 2018 11; 65(7):887-896. Patterson L, Navarro-Gonzalez N, Jay-Russell MT, Aminabadi P, Antaki-Zukoski E, Pires AFA. PMID: 29998551.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCellsPHPublic Health
    26. Tuberculosis Prevalence Among US Crop-Workers, 2000 to 2012: Trends and Contributing Factors. J Occup Environ Med. 2018 07; 60(7):603-611. Medel-Herrero A, Martínez-López B, Silva-Del-Rio N, Pires AF, Edmondson A, Schenker M. PMID: 29271838.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    27. Antimicrobial resistance trends in fecal Salmonella isolates from northern California dairy cattle admitted to a veterinary teaching hospital, 2002-2016. PLoS One. 2018; 13(6):e0199928. Davidson KE, Byrne BA, Pires AFA, Magdesian KG, Pereira RV. PMID: 29953552; PMCID: PMC6023112.
      View in: PubMed   Mentions: 24     Fields:    Translation:AnimalsCells
    28. Association between thermal environment and Salmonella in fecal samples from dairy cattle in midwestern United States. Can J Vet Res. 2016 Jul; 80(3):183-8. Likavec T, Pires AF, Funk JA. PMID: 27408330; PMCID: PMC4924551.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    29. Phenotypic and Genotypic Diversity of Salmonella in Finishing Swine. Foodborne Pathog Dis. 2016 Apr; 13(4):182-9. Pires AF, Funk JA, Habing GG, Bolin C. PMID: 26977814.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCellsPHPublic Health
    30. Assessment of a fluorescent antibody test for the detection of antibodies against epizootic bovine abortion. J Vet Diagn Invest. 2014 Sep; 26(5):622-30. Blanchard MT, Anderson ML, Hoar BR, Pires AF, Blanchard PC, Yeargan BV, Teglas MB, Belshaw M, Stott JL. PMID: 25139792.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    31. Risk factors associated with persistence of Salmonella shedding in finishing pigs. Prev Vet Med. 2014 Sep 01; 116(1-2):120-8. Pires AF, Funk JA, Bolin C. PMID: 25005468.
      View in: PubMed   Mentions: 15     Fields:    Translation:AnimalsCells
    32. Enumeration of salmonella in feces of naturally infected pigs. Foodborne Pathog Dis. 2013 Nov; 10(11):933-7. Pires AF, Funk JA, Lim A, Bolin SR. PMID: 23944750.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    33. Longitudinal study to evaluate the association between thermal environment and Salmonella shedding in a midwestern US swine farm. Prev Vet Med. 2013 Oct 01; 112(1-2):128-37. Pires AF, Funk JA, Manuzon R, Darr M, Zhao L. PMID: 23932067.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    34. Longitudinal study of Salmonella shedding in naturally infected finishing pigs. Epidemiol Infect. 2013 Sep; 141(9):1928-36. Pires AF, Funk JA, Bolin CA. PMID: 23148875; PMCID: PMC9151394.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
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