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Complete list of Dr. Cooper's publications (in reverse chronological order):

University of Arizona Faculty Publications

  1. Schiaffino F, Parker CT, Romaina Cachique L, Garcia Bardales PF, Liu J, Peñataro Yori P, Cooper KK, Pascoe B, Pavlinac P, Houpt E, Paredes Olortegui M, Kosek MN. Robust performance of culture, real-time PCR, and genomic approaches for Shigella serotyping in a pediatric surveillance cohort. 2026. Aug 26;20(8):e0014668. DOI: 10.1371/journal.pntd.0014668.
  2. Truong K, Suarez M, Durigan M, Ewing-Peeples L, Jenkins MC, Kilungo A, Cooper MA, Cooper KK, Lopez GU. Optimization of the Mit1C real-time PCR assay using Bio-Rad CFX96 for the detection of Cyclospora cayetanensis in agricultural waters. 2026. PLoS One. Aug 12;21(8):e0355957. DOI: 10.1371/journal.pone.0355957.
  3. Park R, Rowlands D, Zhu L, Obergh V, Porchas M, Brierley P, Crosby K, Friedman M, Turini T, Patil B, Cooper KK, Ravishankar S. Prevalence of foodborne pathogens and indicator microorganisms on Arizona and California grown commercial cantaloupe melons and in environmental samples. 2026. Food Microbiol. Aug;137:105023. DOI: 10.1016/j.fm.2025.105023.
  4. Romaina Cachique L, Schiaffino F, Paredes Olortegui M, Manzanares K, Pinedo Vasquez T, Castro A, Najarro J, Cooper KK, Mourkas E, Pascoe B, Peñataro Yori P, Parker CT, Kosek MN. Phenotypic resistance of Campylobacter isolates to an extended panel of antibiotics. 2026. Am J Trop Med Hyg. Jul 30;tmpd260268. DOI: 10.4269/ajtmh.26-0268.
  5. Paredes Olortegui M, Schiaffino F, Peñataro Yori P, Colston JM, Mourkas E, Shapiama Lopez WV, Pinedo Vasquez TN, Garcia Bardales PF, Flynn TG, Ramal-Asayag C, Hughes HR, Davis E, Russell BJ, Brault AC, Alegre Palomino YA, Munayco CV, Liu J, Houpt E, Pascoe B, Cooper KK, Parker CT, Kosek MN. Genomic epidemiology of a 2023-2024 Oropouche virus disease outbreak in Iquitos, Peru: descriptive analysis of a case control study for acute febrile illness. 2026. Lancet Reg Health Am. Feb 19;56:101413. DOI: 10.1016/j.lana.2026.101413.
  6. Parker CT, Kathariou S, Miller WG, Huynh S, Pascoe B, Cooper KK. American black bear (Ursus americanus) as a potential host for Campylobacter jejuni. 2025. PLoS One. Sept 9; 20(9):e0331559. DOI: 10.1371/journal.pone.0331559.
  7. Bosquez JM, Parker CT, Pascoe B, Cooper KK. Growth rates and metabolic traits differ by diarrhoeal manifestation in Campylobacter jejuni strains. 2025. J Med Microbiol. Aug; 74(8):002053. DOI: 10.1099/jmm.0.002053.
  8. Kumar NR, Balraj TA, Cooper KK, Prashant A. 2025. Whole-genome sequencing and bioinformatic tools powered by machine learning to identify antibiotic-resistant genes and virulence factors in Escherichia coli from sepsis. Microb Genom. Aug; 11(18):001465. DOI: 10.1099/mgen.0.001465.
  9. Pogreba BK, Austhof E, McFadden CM, Scranton C, Sun X, Vujkovic-Cviji I, Rodriguez D, Falk L, Heslin KM, Arani G, Obergh V, Bessey K, Cooper K. 2025. Determining the incidence, risk factors and biological drivers of irritable bowel syndrome (IBS) as part of the constellation of postacute sequelae of SARS-CoV-2 infection (PASC) outcomes in the Arizona CoVHORT-GI: a longitudinal cohort study. BMJ Open. Jan 30; 15(1):e095093. DOI: 10.1136/bmjopen-2024-095093.
  10. Cooper KK, Mourkas E, Schiaffino F, Parker CT, Pinedo Vasquez TN, Bardales PF, Penataro Yori P, Paredes Olotegui M, Manzanares Villaneuva K, Romaina Cachique L, Silva Delgado H, Hitchings MD, Huynh S, Sheppard SK, Pascoe B, Kosek MN. 2024. Sharing of cmeRABC alleles between C. coli and C. jejuni associated with extensive drug resistance in Campylobacter isolates from infants and poultry in the Peruvian Amazon. mBio, Dec 27:e0205424. DOI:10.1128/mbio.02054-24.  
  11. Schiaffino F, Colston JM, Paredes Olortegui M, Penataro Yori P, Mourkas E, Pascoe B, Lima AAM, Mason CJ, Ahmed T, Kang G, Mduma E, Samie A, Zaidi A, Liu J, Cooper KK, Houpt ER, Parker CT, Lee GO, Kosek MN. 2024. The epidemiology and impact of persistent Campylobacter infections on childhood growth among children 0-24 months of age in resource-limited settings. EClinicalMedicine. Sept 28; 76:102841. DOI: 10.1016/eclinm.2024.102841.
  12. Goforth M, Obergh V, Park R, Porchas M, Brierley P, Turni T, Patil B, Ravishankar S, Huynh S, Parker CT, Cooper KK. 2024. Bacterial diversity of cantaloupes and soil from Arizona and California commercial fields at the point of harvest. PLoS One. Sep 26; 19(9):e0307477. DOI: 10.1371/journal.pone.0307477.
  13. Pascoe B, Futcher G, Pensar J, Bayliss SC, Mourkas E, Calland JK, Hitchings MD, Joseph LA, Lane CG, Greenlee T, Arning N, Wilson DJ, Jolley KA, Corandor J, Maiden MCJ, Parker CT, Cooper KK, Rose EB, Hiett K, Bruce BB, Sheppard SK. 2024. Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data. J Infect. Nov; 89(5):106265. DOI: 10.1016/j.jinf.2024.106265.
  14. Mourkas E, Valdebenito JO, Marsh H, Hitchings MD, Cooper KK, Parker CT, Szekely T, Johansson H, Ellstrom P, Pascoe B, Waldenstrom J, Sheppard SK. 2024. Proximity to humans is associated with antimicrobial-resistant enteric pathogens in wild bird microbiomes. Curr Biol. Sept 9; 34(17):3955-3965.e4. DOI: 10.1016/j.cub.2024.07.059.
  15. Schiaffino F, Parker CT, Garcia Bardales PF, Huynh S, Villanueva K, Mourkas E, Pascoe B, Penataro Yori P, Paredes Olortegui M, Houpt ER, Liu J, Cooper KK, Kosek MN. 2024 Novel rpsK/rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool. PLoS Negl Trop Dis. Mar 1; 18(3):e0012018. DOI: 10.1371/journal.pntd.0012018.
  16. Goforth M, Obergh V, Park R, Porchas M, Crosby KM, Jifron JL, Ravishankar S, Brierley P, Leskovar DL, Turini TA, Schulthesis J, Coolong T, Miller R, Koiwa H, Patil BS, Cooper MA, Huynh S, Parker CT, Guan W, Cooper KK. 2024. Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States. PLoS One, Apr 11; 19(4):e0293861. DOI: 10.1371/journal.pone.0293861. 
  17. Goforth M, Cooper MA, Oliver A, Pinzon J, Skots M, Obergh V, Suslow TV, Flores GE, Huynh S, Parker CT, Mackelprang R, Cooper KK. 2024. Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons. PLoS One, Apr 16; 19(4):e0297453. DOI: 10.1371/journal.pone.0297453.
  18. Schiaffino F, Parker CT, Paredes Olortegui M, Pascoe B, Manzanares Villanueva K, Garcia Bardales PF, Mourkas E, Huynh S, Penataro Yori P, Romaina Cachique L, Gray HK, Salvatierra G, Silva Delgado H, Sheppard SK, Cooper KK, Kosek MN. 2024. Genomic resistant determinants of multidrug resistant Campylobacter spp. isolates in Peru. J Glob Antimicrob Resist, Jan 23:S22137165(24)00017-1.
  19. Penataro Yori P, Paredes Olortegui M, Schiaffino F, Colston JM, Vasquez T, Garcia Bardales PF, Shapiama Lopez V, Zegarra Paredes LF, Perez K, Curico G, Flynn T, Zhang J, Ramal Asayag C, Meza Sanchez G, Silva Delgado H, Casapia Morales M, Casanova W, Jiu B, Oberhelman R, Munayco Escate C, Silver R, Henao O, Cooper KK, Liu J, Houpt ER, Kosek MN. 2023. Etiology of acute febrile illness in the Peruvian Amazon as determined by modular formatted quantitative PCR: a protocol for RIVERA, a health facility-based case-control study. BMC Public Health, Apr 11; 23(1):674. DOI: 10.1186/s12889-023-15619-6.
  20. Gabbert AD, Mydosh JL, Talukdar PK, Gloss LM, McDermott JE, Cooper KK, Clair GC, Konkel ME. 2023. The Missing Pieces: the role of secretion systems in Campylobacter jejuni virulence. Biomolecules, Jan 9; 13(1):135. DOI: 10.3390/biom13010135.
  21. Garcia Bardales PF, Schiaffino F, Huynh S, Paredes M, Penataro Yori P, Pinedo Vasquez T, Manzanares Villaneuva K, Curico Huansi GE, Shapiama Lopez WV, Cooper KK, Parker CT, Kosek MN. 2022. “Candidatus Campylobacter infans” detection is not associated with diarrhea in children under the age of 2 in Peru. PLoS Negl Trop Dis. Oct 17:16(10):e0010869. DOI: 10.1371/journal.pntd.0010869.
  22. Sen A, Goforth M, Cooper KK, Anakk S. 2022. Deletion of constitutive Androstane Receptor led to intestinal alterations and increased Imidacloprid in murine liver. J Endocrine Society. 6(12):1-9. DOI: 10.1210/jendso/bvac145.
  23. Parker CT, Schiaffino F, Huynh S, Paredes Olortegui M, Penataro Yori P, Garcia Bardales PF, Pinedo Vasquez T, Curico Huansi GE, Manzanares Villanueva K, Shapiama Lopez WV, Cooper KK, Kosek MN. 2022. Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species. PLoS Negl Trop Dis. Oct 4:16(10):e0010815. DOI: 10.1371/journal.pntd.0010815.
  24. Austhof E, Bell ML, Riddle MS, Catalfamo C, McFadden C, Cooper K, Scallan Walter E, Jacobs E, Pogreba-Brown K. 2022. Persisting gastrointestinal symptoms and post-infectious bowel syndrome following SARS-CoV-2 infection: results from the Arizona CoVHORT. Epidemiol Infect. Jul 8:150:e136. DOI: 10.1017/ S0950268822001200.
  25. Luna E, Parkar S, Kirmiz N, Hartel S, Hearn E, Hossine M, Kurdian A, Mendoza C, Orr K, Padilla L, Ramirez K, Salcedo P, Serrano E, Choudhry B, Paulchakrabarti M, Parker C, Cooper K, Flores G. 2021. Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent. Appl Envrion Microbiol. Oct 20: AEM0148721. DOI: 10.1128/AEM.01487-21.
  26. Heikema AP, Strepis N, Horst-Kreft D, Huynh S, Zomer AL, Kelly DJ, Cooper KK, Parker CT. 2021. Biomolecule sulfation and novel methylations related to Guillain-Barre syndromeassociated C. jejuni serotype HS:19. Microb Genom. Nov: 7(11). DOI: 10.1099/mgen.0.000660.
  27. Achtman M, Van den Broeck F, Cooper KK, Lemey P, Parker CT, Zhou Z, et al. 2021. Genomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature. PLoS Genet. 17(9):e1009820. DOI: 10.1371/journal.pgen.1009820.
  28. Katiyar N, Ramadoss N, Gupta D, Pakala, SB, Cooper K, Basu C. 2021. Transcriptomic profiling of Paulownia elongata in response to heat stress. Plant Gene. 28:100330. DOI: 10.1016/j.plgene.2021.100330.
  29. Crippen C, Zhou B, Andresen S, Patry R, Muszynski A, Parker C, Cooper KK, Szymanski C. 2021. RNA and sugars, unique properties of bacteriophages infecting multidrug resistant Acinetobacter radioresistens strain LH6. Viruses. 13(8):1652. DOI: 10.3390/v13081652.
  30. Parker CT, Huynh S, Alexander A, Oliver AS, Cooper KK. 2021. Genomic characterization of Salmonella Typhimurium DT104 strains associated with cattle and beef products. Pathogens. 10(5):529. DOI: 10.3390/pathogens10050529.
  31. Parker CT, Cooper KK, Schiaffino F, Miller WG, Huynh S, Gray HK, Olortegui MP, Bardales PG, Trigoso DR, Penataro-Yori P, Kosek MN. 2021. Genomics characterization of guinea pig (Cavia porcellus) adapted Campylobacter jejuni. Front Cell Infect Microbiol. 11:607747. DOI: 10.3389/fcimb.2021.607747.
  32. Arias DB, Gomez Pinto KA, Cooper KK, Summers ML. 2020. Transcriptomic analysis of cyanobacterial alkane overproduction reveals stress-related genes and inhibitors of lipid droplet formation. Microb Genom. 6(10):mgen000432 DOI: 10.1099/mgen.0.000432.
  33. Pascoe B, Schiaffino F, Murray S, Bayliss SC, Hitchings MD, Mourkas E, Meric G, Calland JK, Burga R, Penataro Yori P, Jolley KA, Cooper KK, Parker CT, Paredes Olortegui M, Kosek MN, Sheppard SK. 2020. Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon. PLoS Neglected Tropical Diseases. 14(8):e0008533.DOI: 10.1371/journal.pntd.0008533
  34. Bian X, Garber JM, Cooper KK, Huynh S, Jones J, Mills MK, Rafala D, Nasrin D, Kotloff KL, Parker CT, Tennant SM, Miller WG, Szymanski CM. 2019. Campylobacter abundance in breastfed infants and identification of a new species in the Global Enterics Multicenter Study. mSphere. 5(1):e00735-19 DOI: 10.1128/mSphere.00735-19.
  35. Ruiz C, McCarley A, Espejo ML, Cooper KK, Harmon DE. 2019. Comparative genomics reveals a well-conserved intrinsic resistome in the emerging multidrug-resistant pathogen Cupriavidus gilardii. mSphere. 4(5):e00631-19. DOI: 10.1128/mSphere.00631-19.
  36. Parker CT, Cooper KK, Huynh S, Smith TP, Bono JL, Cooley M. 2018. Genome sequences of eight Shiga toxin-producing Escherichia coli strains isolated from a produce-growing region in California. Microbiology Resource Announcements. 7(1):e00807-18. DOI: 10.1128/MRA.00807- 18.
  37. Pinoargote G, Flores, G, Cooper K, Ravishankar S. 2018. Effects on survival and bacterial community composition of the aquaculture water and gastrointestinal tract of shrimp (Litopenaeus vannamei) exposed to probiotic treatments after an induced infection of acute hepatopancreatic necrosis disease. Aquaculture Research. 49:3270-3288. DOI: 10.1111/are.13791.
  38. Oliver A, Kay M, Cooper KK. 2018. Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC Genomics. 19(1):310. DOI: 10.1186/s12864-018- 4635-8.
  39. Seuylemezian A, Vaishampayan P, Cooper K, Venkateswaran K. 2018. Draft genome sequences of Acinetobacter and Bacillus strains isolated from spacecraft-associated surfaces. Genome Announcements. 6(6):e01554-17. DOI: 10.1128/genomeA.01554-17.
  40. Seuylemezian A, Cooper K, Schubert W, Vaishampayan P. 2018. Draft genome sequences of 12 dryheat-resistant Bacillus strains isolated from the cleanrooms where the Viking Spacecraft were assembled. Genome Announcements. 6(12):e00094-18. DOI: 10.1128/genomeA.00094-18.

Non-University of Arizona Faculty Publications

  1. Gorski L, Huynh S, Cooper KK, Parker CT. Complete Genomic Sequences of Two Salmonella entericasubsp. enterica Serogroup C2 (O:6,8) Strains from Central California. 2017. Genome Announc. Nov 16;5(46). DOI: 10.1128/genomeA.01234-17.
  2. Pascoe B, Méric G, Yahara K, Wimalarathna H, Murray S, Hitchings MD, Sproston EL, Carrillo CD, Taboada EN, Cooper KK, Huynh S, Cody AJ, Jolley KA, Maiden MCJ, McCarthy ND, Didelot X, Parker CT, Sheppard SK. Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations. 2017. Mol Ecol. Sep;26(17):4497-4508. DOI: 10.1111/mec.14176.
  3. Chaires M, Gupta D, Joshee N, Cooper KK, Basu C. RNA-seq analysis of the salt stress-induced transcripts in fast-growing bioenergy tree, Paulownia elongata. 2017. J Plant Interactions. March; 12(1):128-136. DOI: 10.1080/17429145.2017.1298851.
  4. Parker CT, Huynh S, Gorski L, Cooper KK, Miller WG. Complete Genome Sequences of Two Outbreak Strains of Salmonella enterica subsp. enterica Serovar Thompson Associated with Cilantro. 2015. Genome Announc. Nov 19;3(6). DOI: 10.1128/genomeA.01365-15.  
  5. Parker CT, Huynh S, Heikema AP, Cooper KK, Miller WG. Complete Genome Sequences of Campylobacter jejuni Strains RM3196 (233.94) and RM3197 (308.95) Isolated from Patients with Guillain-Barré Syndrome. 2015. Genome Announc. Nov 5;3(6). DOI: 10.1128/genomeA.01312-15.
  6. Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ. Complete Genome Sequences of Two Escherichia coli O145:H28 Outbreak Strains of Food Origin. 2014. Genome Announc. May 22;2(3). DOI: 10.1128/genomeA.00482-14.
  7. Cooper KK, Mandrell RE, Louie JW, Korlach J, Clark TA, Parker CT, Huynh S, Chain PS, Ahmed S, Carter MQ. Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7. 2014. BMC Genomics. Jan 10;15:17. DOI: 10.1186/1471-2164-15-17.  
  8. Cooper KK, Songer JG, Uzal FA. Diagnosing clostridial enteric disease in poultry. 2013. J Vet Diagn Invest. May;25(3):314-27. DOI: 10.1177/1040638713483468.
  9. Cooper KK, Bueschel DM, Songer JG. Presence of Clostridium perfringens in retail chicken livers. 2013. Anaerobe. Jun;21:67-8. DOI: 10.1016/j.anaerobe.2013.03.013.
  10. Cooper KK, Cooper MA, Zuccolo A, Joens LA. Re-sequencing of a virulent strain of Campylobacter jejuni NCTC11168 reveals potential virulence factors. 2013. Res Microbiol. Jan;164(1):6-11. DOI: 10.1016/j.resmic.2012.10.002.
  11. Theoret JR, Cooper KK, Zekarias B, Roland KL, Law BF, Curtiss R 3rd, Joens LA. The Campylobacter jejuni Dps homologue is important for in vitro biofilm formation and cecal colonization of poultry and may serve as a protective antigen for vaccination. 2012. Clin Vaccine Immunol. Sep;19(9):1426-31. DOI: 10.1128/CVI.00151-12.
  12. Coursodon CF, Glock RD, Moore KL, Cooper KK, Songer JG. TpeL-producing strains of Clostridium perfringens type A are highly virulent for broiler chicks. 2012. Anaerobe. Feb;18(1):117-21. DOI: 10.1016/j.anaerobe.2011.10.001.
  13. Theoret JR, Cooper KK, Glock RD, Joens LA. A Campylobacter jejuni Dps homolog has a role in intracellular survival and in the development of campylobacterosis in neonate piglets. 2011. Foodborne Pathog Dis. Dec;8(12):1263-8. DOI: 10.1089/fpd.2011.0892.
  14. Cooper KK, Cooper MA, Zuccolo A, Law B, Joens LA. Complete genome sequence of Campylobacter jejuni strain S3. 2011. J Bacteriol. Mar;193(6):1491-2. DOI: 10.1128/JB.01475-10.
  15. Cooper KK, Theoret JR, Stewart BA, Trinh HT, Glock RD, Songer JG. Virulence for chickens of Clostridium perfringens isolated from poultry and other sources. 2010. Anaerobe. Jun;16(3):28992. DOI: 10.1016/j.anaerobe.2010.02.006.
  16. Cooper KK, Songer JG. Virulence of Clostridium perfringens in an experimental model of poultry necrotic enteritis. 2010. Vet Microbiol. May 19;142(3-4):323-8. DOI: 10.1016/j.vetmic.2009.09.065.
  17. Cooper KK, Songer JG. Necrotic enteritis in chickens: a paradigm of enteric infection by Clostridium perfringens type A. 2009. Anaerobe. Feb-Apr;15(1-2):55-60. DOI: 10.1016/j.anaerobe.2009.01.006.
  18. Cooper KK, Trinh HT, Songer JG. Immunization with recombinant alpha toxin partially protects broiler chicks against experimental challenge with Clostridium perfringens. 2009. Vet Microbiol. Jan 1;133(1-2):92-7. DOI: 10.1016/j.vetmic.2008.06.001.