Publications

2023

Di Francesco J, Ittle A, Mconnel C, Adams R, Busch R, Pereira RV, Lehenbauer TW, Martínez-López B, Pires AFA . 2023. Extending Knowledge on Biosecurity in Small-scale and Backyard Systems in the United States Journal of Extension (in-press) MS#4247

Devarajan N, Weller DL, …..Pires AFA…..Wall G, Karp, DS, 2023. Evidence for the efficacy of pre-harvest agricultural practices in mitigating food-safety risks to fresh produce in North America. Frontiers in Sustainable Food Systems 7. https://doi.org/10.3389/fsufs.2023.1101435

Chiarella C, Lamoureaux Y, Pires, A FA et al. A preliminary assessment of food policy obstacles in California’s produce recovery networks. Agric Hum Values. 2023. https://doi.org/10.1007/s10460-022-10407-1

Pires AFA, Ramos T, Baron JN, Millner PD, Pagliari P, Hutchinson M,..., Sciligo AR, Jay-Russell M Risk Factors Associated with the Prevalence of Shiga-toxin-producing E. coli in Manured Soils on Certified Organic Farms in Four Regions of the USA. 2023 Front. Sustain. Food Syst., Agro-Food Safety. 7 https://doi.org/10.3389/fsufs.2023.1125996

Chandler-Khayd C, Di Francesco J, Baron JN, Ramos TDM, Aminabadi P, Jay-Russell MT, Haghani V, Millner PD, Pagliari PH, Hutchinson M, Kenney A, Hashem F, Martínez-López B, Bihn EA, Clements DP, Shade JB, Sciligo AR, Pires AFA, 2023. Risk factors associated with the prevalence of Listeria monocytogenes in manured soils on certified organic farms in four regions of the United States. Frontiers in Sustainable Food Systems 7. | https://doi.org/10.3389/fsufs.2023.1222192

2022

Lee K, Pereira RV, Martínez-López B, Busch RC, Pires AFA. 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 Nov 21;17(11):e0277897. doi: 10.1371/journal.pone.0277897.

Cheong, S., Di Francesco, J., Lee, K., Van Vleck Pereira, R., Black, R., Karle, B., Lema, M., Pires, A.F.A., 2022. Survey of Management Practices and Farmers’ Perceptions of Diseases on Organic Dairy Cattle Farms in California. Animals. 2022; 12(19):2526. https://doi.org/10.3390/ani12192526

Patterson L, Belkhiria J, Martínez-López B, Pires AFA. 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 Jun 28;17(6):e0270500. doi: 10.1371/journal.pone.0270500. PMID: 35763526; PMCID: PMC9239460.

Patterson L, Navarro-Gonzalez N, Jay-Russell MT, Aminabadi P, Pires AFA. Risk factors of Shiga toxin-producing Escherichia coli in livestock raised on diversified small-scale farms in California. Epidemiol Infect. 2022. Jun 1;150:e125. doi: 10.1017/S0950268822001005. PMID: 35641482; PMCID: PMC9274804.  

2021

De Melo Ramos T, Jay-Russell M, Millner PD, Baron JN, Stover J, Pagliari P, Hutchinson M....Haghani V,.... Pires AFA, 2021. Survival and Persistence of Foodborne Pathogens in Manure-Amended Soils and Prevalence on Fresh Produce in Certified Organic Farms: A Multi-Regional Baseline Analysis (2021). Front. Sustain. Food Syst. 5:674767. doi: 10.3389/fsufs.2021.674767https://doi.org/10.3389/fsufs.2021.674767

O’Hara KC, Pires AFA, Martínez-López B, Moore D., 2021. Evaluating the association between climatic factors and sheep condemnations in the United States using cluster analysis and spatio-temporal modeling. Preventive Veterinary Medicine . https://doi.org/10.1016/j.prevetmed.2021.105342

Samaddar S, Karp DS, Schmidt R, Devarajan N, McGarvey JA, Pires AFA, Scow K, 2021. Role of soil in the regulation of human and plant pathogens: soils’ contributions to people Philosophical Transactions of the Royal Society (Phil. Trans. R. Soc.) 376: 20200179.20200179 http://doi.org/10.1098/rstb.2020.0179.

Basbas C, Byrne BA, Chigerwe M, Escobar E, Hodzic E, Pires AFA, Pereira RV, 2021. Detection of Cephalosporin and Fluoroquinolone Resistance Genes via Novel Multiplex qPCR in Fecal Salmonella Isolates from Northern Californian Dairy Cattle, 2002-2016 Frontiers in Microbiology, 12:184. 15 February 2021 | https://doi.org/10.3389/fmicb.2021.601924

Samaddar S, Karp DS, Schmidt R, Devarajan N, McGarvey JA, Pires AFA, Scow K, 2021. Role of soil in the regulation of human and plant pathogens: soils’ contributions to people Philosophical Transactions of the Royal Society (Phil. Trans. R. Soc.) 376: 20200179.20200179 http://doi.org/10.1098/rstb.2020.0179. 

O’Hara KC, Pires AFA, Martínez-López B, Moore D., 2021. Evaluating the association between climatic factors and sheep condemnations in the United States using cluster analysis and spatio-temporal modeling. Preventive Veterinary Medicine. https://doi.org/10.1016/j.prevetmed.2021.105342 

2020

Pires AFA, Stover J,  Kukielka EA,  Haghani V, De Melo Ramos T, Paieman, A; Jay-Russell M., 2020. Salmonella and generic E. coli prevalence in meat and produce sold at farmers markets in Northern California. Journal of Food Protection 83(11): 1934-1940 https://doi.org/10.4315/JFP-20-079 . Feature article of November issue

Pires AFA, Peterson A, Baron J, Adams R, Moore D. 2020. Assessment of veterinarians’ engagement with backyard poultry and small-scale livestock production in four western states. JAVMA July 15, 2020, Vol. 257, No. 2, Pages 196-209.

Pandey, P., S. K. Vidyarthi, V. Vaddella, C. Venkitasamy, M. Pitesky, B. Weimer, and Pires AFA, 2020. Improving Biosecurity Procedures to Minimize the Risk of Spreading Pathogenic Infections After Carcass Recycling. Frontiers in Microbiology 2020; 11:623. https://doi.org/10.3389/fmicb.2020.00623

Pires AFA, Kukielka EA,  Haghani V, Stover J, De Melo Ramos T, Jay-Russell M, 2020. A Survey of Farmers Market Managers in California: Food Safety Perspectives. Journal of Extension, 58(5). Article # v58-5a7

2019

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, 2019. Association between herd management practices and antimicrobial resistance in Salmonella spp. from cull dairy cattle in Central California. PeerJ 7:e6546 https://doi.org/10.7717/peerj.6546

Pires AFA, Peterson A, Baron J, Adams R, Martínez-López B, Moore D., 2019. Small-scale livestock and backyard owners needs assessment in western United States. PLoS One 2019 Feb 14;14(2): e0212372. doi: 10.1371/journal.pone.0212372

Pires AFA, Patterson L, Aminabadi P, Kukielka E, Navarro-Gonzalez N, Jay-Russell M., 2019. Prevalence and Risk factors associated with Campylobacter and Salmonella in livestock raised on diversified small-scale farms in California. Epidemiology and Infection 147, e321

De Melo Ramos T, Jay-Russell M, Millner PD, Shade J, Sorge US, Hutchinson M, Lilley J, Pires AFA., 2019. Assessment of organic produce farming research and outreach needs regarding food safety risks and raw manure and compost applications. Frontiers in Sustainable Food Systems 3:73 https://doi.org/10.3389/fsufs.2019.00073

2018

Simoes J, Pires AFA., 2018. Reproductive disorders in Portuguese Serrana goats and its effects on milk production. Revista Colombiana de Ciencias Pecuarias (RCCP), 31(1): 64-71.

Medel-Herrero A, Martinez-Lopez B, Silva-del-Rio, Pires AFA, Edmondson A, Schenker M., 2018. Tuberculosis Prevalence Among US Crop-Workers, 2000 to 2012: Trends and Contributing Factors. Journal of Occupational & Environmental Medicine, 60(7): 603-611.

Patterson L, Navarro-Gonzalez N, Aminabadi P, Jay-Russell M, Antaki E, Pires AFA, 2018. Persistence of Escherichia coli in the soil of an organic mixed crop-livestock farm that integrates sheep grazing within vegetable fields. Zoonoses Public Health, 65(7): 887-896.

Pires AFA, Millner PD, Baron J, Jay-Russell M., 2018. Assessment of Current Practices of Organic Farmers Regarding Biological Soil Amendments of Animal Origin in a Multi-Regional US Study. Food Protection Trends 38 (5) 347-362

Davidson KE; Byrne, BA; Pires AFA; Magdesian KG; Pereira RV, 2018. Antimicrobial resistance trends in fecal Salmonella isolates from northern California dairy cattle admitted to a veterinary teaching hospital, 2002-2016. PLoS One 13(6):e0199928 doi:10.1371/journal.pone.0199928.

Pires AFA, Millner PD, Baron J, Jay-Russell M. Assessment of Current Practices of Organic Farmers Regarding Biological Soil Amendments of Animal Origin in a Multi-Regional US Study. Food Protect. Trends 2018. 38 (5) 347-362 https://www.foodprotection.org/publications/food-protection-trends/archive/2018-09-assessment-of-current-practices-of-organic-farmers-regarding-biological-soil-amendments-of-a/

2016

Pires AFA, Funk JA, Habing G, Bolin C., 2016. Phenotypic and genotypic diversity of Salmonella in finishing swine. Foodborne Pathogens and Diseases,13(4): 182-9.

Likavec T, Pires AFA, Funk JA., 2016. Association between thermal environment and Salmonella in floor fecal samples from a Midwestern US dairy. Canadian Journal of Veterinary Research 80(3): 183-8.

2015

Streider-Barboza C, Zondlak A, Kayitsinga J, Pires AFA, Contreas GA., 2015. Lipid mobilization assessment in transition dairy cattle using ultrasound biomarkers. Livestock Science, 177: 159-64.

2014

Blanchard MT, Anderson ML, Hoar BR, Pires AFA, Blanchard PC, Yeargan BV, Teglas MB, Belshaw M, Stott JL, 2014. Assessment of a fluorescent antibody test for the detection of antibodies against epizootic bovine abortion. Journal of Veterinary Diagnostic Investigation, 26(5): 622-30.

2019

Jennifer Sowerwine, Christina Oatfield, Rob Bennaton, Alda Pires, Racehl Surls, Valerie Borel, Andre Biscaro: California Urban Agriculture Food Safety Guide: Laws and Standard Operating Procedures for Farming Safely in the City. California Urban Agriculture Food Safety Guide, UC Berkeley, UC Cooperative Extension, and the Sustainable Economies Law Center. (UC ANR peer-reviewed)

2017

Maier G, Pires AFA, Patterson L: The Risk for Q Fever in Public Settings (Chapter 15), Simoes J; Anastacio S; Jorge da Silva G, (ed), Principles and Practice of Q-Fever: The One Health Paradigm, NOVA.

Pires AFA, Patterson L, Maier G.: Coxiella burnetii Implications for Food Safety (Chapter 16), Simoes J; Anastacio S; Jorge da Silva G, (ed), Principles and Practice of Q-Fever: The One Health Paradigm, NOVA.