Jonathan Harris, PhD
Associate Professor, Pediatrics-Pulmonary Medicine

Publications

• Harris JK, Wagner BD, Robertson CE, Stevens MJ, Lingard C, Borowitz D, Leung DH, Heltshe SL, Ramsey BW, Zemanick ET. Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen. J Cyst Fibros. 2023 Jul;22(4):644-651. PubMed PMID: 37137746
• O'Connor JB, Wagner BD, Harris JK, Frank DN, Clabots DE, Laguna TA. Detection and identification of fungi in the lower airway of children with and without cystic fibrosis. Front Microbiol. 2023;14:1119703. PubMed PMID: 36846802
• Furuta GT, Fillon SA, Williamson KM, Robertson CE, Stevens MJ, Aceves SS, Arva NC, Chehade M, Collins MH, Davis CM, Dellon ES, Falk GW, Gonsalves N, Gupta SK, Hirano I, Khoury P, Leung J, Martin LJ, Menard-Katcher P, Mukkada VA, Peterson K, Spergel JM, Wechsler JB, Yang GY, Rothenberg ME, Harris JK. Mucosal Microbiota Associated With Eosinophilic Esophagitis and Eosinophilic Gastritis. J Pediatr Gastroenterol Nutr. 2023 Mar 1;76(3):347-354. PubMed PMID: 36525669
• Leroue MK, Williamson KM, Curtin PC, Sontag MK, Wagner BD, Ambroggio L, Bixby M, Busgang SA, Murphy SE, Peterson LA, Vevang KR, Sipe CJ, Kirk Harris J, Reeder RW, Locandro C, Carpenter TC, Maddux AB, Simões EAF, Osborne CM, Robertson CE, Langelier C, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Mourani PM. Tobacco smoke exposure, the lower airways microbiome and outcomes of ventilated children. Pediatr Res. 2023 Aug;94(2):660-667. PubMed PMID: 36750739
• Osborne CM, Langelier C, Kamm J, Williamson K, Ambroggio L, Reeder RW, Locandro C, Kirk Harris J, Wagner BD, Maddux AB, Caldera S, Lyden A, Soesanto V, Simões EAF, Leroue MK, Carpenter TC, Hall MW, Zuppa AF, Carcillo JA, Meert KL, Pollack MM, McQuillen PS, Notterman DA, DeRisi J, Mourani PM. Viral Detection by Reverse Transcriptase Polymerase Chain Reaction in Upper Respiratory Tract and Metagenomic RNA Sequencing in Lower Respiratory Tract in Critically Ill Children With Suspected Lower Respiratory Tract Infection. Pediatr Crit Care Med. 2023 Sep 21. [Epub ahead of print] PubMed PMID: 37732845
• Wagner BD, Zemanick ET, Sagel SD, Robertson CE, Stevens MJ, Mayer-Hamblett N, Retsch-Bogart G, Ramsey BW, Harris JK. Limited effects of azithromycin on the oropharyngeal microbiome in children with CF and early pseudomonas infection. BMC Microbiol. 2023 Oct 27;23(1):312. PubMed PMID: 37891457
• Tsitsiklis A, Osborne CM, Kamm J, Williamson K, Kalantar K, Dudas G, Caldera S, Lyden A, Tan M, Neff N, Soesanto V, Harris JK, Ambroggio L, Maddux AB, Carpenter TC, Reeder RW, Locandro C, Simões EAF, Leroue MK, Hall MW, Zuppa AF, Carcillo J, Meert KL, Sapru A, Pollack MM, McQuillen PS, Notterman DA, Dean JM, Zinter MS, Wagner BD, DeRisi JL, Mourani PM, Langelier CR. Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics. Lancet Microbe. 2022 Apr;3(4):e284-e293. PubMed PMID: 35544065
• O'Connor JB, Mottlowitz M, Kruk ME, Mickelson A, Wagner BD, Harris JK, Wendt CH, Laguna TA. Network Analysis to Identify Multi-Omic Correlations in the Lower Airways of Children With Cystic Fibrosis. Front Cell Infect Microbiol. 2022;12:805170. PubMed PMID: 35360097
• O’Connor, JB, Wagner, BD, Harris, JK and Laguna, TA. Comparison of neutrophil elastase to the lower airway microbiome in children with cystic fibrosis. 2022. Am. J. Respir. Crit. Care Med. 203:A1992.
• O’Connor, JB, Wagner, BD, Harris, JK and Laguna TA. Relationship between inflammation and bacterial ecology in bronchoalveolar lavage fluid from the cystic fibrosis airway. 2022. J. Cystic Fibrosis. 21:S260.
• Harris, JK, Graham, B, Zemanick, ET and Wagner, BD. Evaluation of bacterial detection by microbial cell-free deoxyribonucleic acid using plasma collected during admission for cystic fibrosis pulmonary exacerbation. 2022. J. Cystic Fibrosis. 21:S272.
• Williamson KM, Wagner BD, Robertson CE, Stevens MJ, Sontag MK, Mourani PM, Harris JK. Modified PCR protocol to increase sensitivity for determination of bacterial community composition. Microbiome. 2021 Apr 13;9(1):90. PubMed PMID: 33849648
• Stanish LF, Sherwood OA, Lackey G, Osborn S, Robertson CE, Harris JK, Pace N, Ryan JN. Microbial and Biogeochemical Indicators of Methane in Groundwater Aquifers of the Denver Basin, Colorado. Environ Sci Technol. 2021 Jan 5;55(1):292-303. PubMed PMID: 33296185
• Khalaf RT, Furuta GT, Wagner BD, Robertson CE, Andrews R, Stevens MJ, Fillon SA, Zemanick ET, Harris JK. Influence of Acid Blockade on the Aerodigestive Tract Microbiome in Children With Cystic Fibrosis. J Pediatr Gastroenterol Nutr. 2021 Apr 1;72(4):520-527. PubMed PMID: 33394582
• Mourani PM, Sontag MK, Williamson KM, Harris JK, Reeder R, Locandro C, Carpenter TC, Maddux AB, Ziegler K, Simões EAF, Osborne CM, Ambroggio L, Leroue MK, Robertson CE, Langelier C, DeRisi JL, Kamm J, Hall MW, Zuppa AF, Carcillo J, Meert K, Sapru A, Pollack MM, McQuillen P, Notterman DA, Dean JM, Wagner BD. Temporal airway microbiome changes related to ventilator-associated pneumonia in children. Eur Respir J. 2021 Mar;57(3). PubMed PMID: 33008935
• Mourani PM, Sontag MK, Williamson KM, Harris JK, Reeder R, Locandro C, Carpenter TC, Maddux AB, Ziegler K, Simões EAF, Osborne CM, Ambroggio L, Leroue MK, Robertson CE, Langelier C, DeRisi JL, Kamm J, Hall MW, Zuppa AF, Carcillo J, Meert K, Sapru A, Pollack MM, McQuillen P, Notterman DA, Dean JM, Wagner BD. Temporal airway microbiome changes related to ventilator associated pneumonia in children. Eur Respir J. 2020 Oct 2. [Epub ahead of print] PubMed PMID: 33008935
• Jewell MP, Saccomano SC, David AA, Harris JK, Zemanick ET, Cash KJ. Nanodiagnostics to monitor biofilm oxygen metabolism for antibiotic susceptibility testing. Analyst. 2020 Jun 7;145(11):3996-4003. PubMed PMID: 32342070
• Clabots, D, Holt, JW, Robertson, CE, Zemanick, ET, Frank, DN and Harris, JK. Comparison of bacterial and fungal communities in bronchoalveolar lavage using small subunit ribosomal RNA. 2020. Am. J. Respir. Crit. Care Med. 201:A2653.
• O’Connor, JB, Wright, JC, Wagner, BD, Harris, JK and Laguna, TA. Divergence of the bacterial communities in the lower airways of cystic fibrosis patients in early childhood. 2020. Am. J. Respir. Crit. Care Med. 201:A7456.
• Leroue, M, Sontag, M, Williamson, K, Wagner, B, Ambroggio, L, Harris, JK, Reeder, R, Locandro, C, Carpenter, TC, Maddux, AB, Simoes, E, Osborne, CM, Langelier, C, Kamm, J, DeRisi, J, Hall, MW, Zuppa, A, Carcillo, J, Meert, K, Sapru, A, Pollack, M, McQuillin, P, Tamburro, R, Dean, JM and Mourani, PM. The relationship of parental reports of smoke exposure with the lower airway microbiome and clinical outcomes in critically ill, mechanically ventilated children. 2020. Am. J. Respir. Crit. Care Med. 201:A7165.
• Khalaf, R, Furuta, G, Wagner, B, Andrews, R, Robertson, C, Zemanick, E and Harris, J. The effect of acid blockade on microbiota and inflammation in cystic fibrosis. 2020. J. Ped. Gastroenterol. Nutr. 71:S445-6.
• O’Connor, JB, Wright, JC, Wagner, BD, Harris, JK and Laguna, TA. Divergence of the bacterial communities in the lower airways of cystic fibrosis patients in early childhood. 2020. Pediatric Pulmonol Suppl. 55:S179-S180.
• Khalaf, R, Furuta, G, Wagner, B, Robertson, C, Andrews, R, Stevens, M, Fillon, S, Zemanick, ET and Harris, JK. Acid blockade effects on microbiota and inflammation in CF. 2020. Pediatric Pulmonol Suppl. 55: S124-125.
• Harris JK, Wagner BD, Zemanick ET, Robertson CE, Stevens MJ, Heltshe SL, Rowe SM, Sagel SD. Changes in Airway Microbiome and Inflammation with Ivacaftor Treatment in Patients with Cystic Fibrosis and the G551D Mutation. Ann Am Thorac Soc. 2019 Oct 11. [Epub ahead of print] PubMed PMID: 31604026
• Deterding RR, Wagner BD, Harris JK, DeBoer EM. Pulmonary Aptamer Signatures in Children's Interstitial and Diffuse Lung Diseases. Am J Respir Crit Care Med. 2019 Aug 13. [Epub ahead of print] PubMed PMID: 31409098
• Wagner BD, Sontag MK, Harris JK, Miller JI, Morrow L, Robertson CE, Stephens MJ, Poindexter BB, Abman SH, Mourani PM. Prenatal complications are associated with the postnatal airway host response and microbiota in intubated preterm infants. J Matern Fetal Neonatal Med. 2019 May;32(9):1499-1506. PubMed PMID: 29157044
• DeBoer EM, Wagner BD, Popler J, Harris JK, Zemanick ET, Accurso FJ, Sagel SD, Deterding RR. Novel Application of Aptamer Proteomic Analysis in Cystic Fibrosis Bronchoalveolar Lavage Fluid. Proteomics Clin Appl. 2019 May;13(3):e1800085. PubMed PMID: 30431231
• Jewell MP, Galyean AA, Kirk Harris J, Zemanick ET, Cash KJ. Luminescent Nanosensors for Ratiometric Monitoring of Three-Dimensional Oxygen Gradients in Laboratory and Clinical Pseudomonas aeruginosa Biofilms. Appl Environ Microbiol. 2019 Oct 15;85(20). PubMed PMID: 31420335
• DeBoer EM, Wagner BD, Popler J, Harris JK, Zemanick ET, Accurso FJ, Sagel SD, Deterding RR. Novel Application of Aptamer Proteomic Analysis in Cystic Fibrosis Bronchoalveolar Lavage Fluid. Proteomics Clin Appl. 2018 Nov 15;:e1800085. [Epub ahead of print] PubMed PMID: 30431231
• Hull NM, Rosenblum JS, Robertson CE, Harris JK, Linden KG. Succession of toxicity and microbiota in hydraulic fracturing flowback and produced water in the Denver-Julesburg Basin. Sci Total Environ. 2018 Dec 10;644:183-192. PubMed PMID: 29981518
• Wagner BD, Grunwald GK, Zerbe GO, Mikulich-Gilbertson SK, Robertson CE, Zemanick ET, Harris JK. On the Use of Diversity Measures in Longitudinal Sequencing Studies of Microbial Communities. Front Microbiol. 2018;9:1037. PubMed PMID: 29872428
• Rosen BH, Evans TIA, Moll SR, Gray JS, Liang B, Sun X, Zhang Y, Jensen-Cody CW, Swatek AM, Zhou W, He N, Rotti PG, Tyler SR, Keiser NW, Anderson PJ, Brooks L, Li Y, Pope RM, Rajput M, Hoffman EA, Wang K, Harris JK, Parekh KR, Gibson-Corley KN, Engelhardt JF. Infection Is Not Required for Mucoinflammatory Lung Disease in CFTR-Knockout Ferrets. Am J Respir Crit Care Med. 2018 May 15;197(10):1308-1318. PubMed PMID: 29327941
• Stanish LF, Hull NM, Robertson CE, Harris JK, Stevens MJ, Spear JR, Pace NR. Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA. PLoS One. 2016 Jun 30;11(6):e0157966. PubMed PMID: 27362708
• Johnson EJ, Zemanick ET, Accurso FJ, Wagner BD, Robertson CE, Harris JK. Molecular Identification of Staphylococcus aureus in Airway Samples from Children with Cystic Fibrosis. PLoS One. 2016 Jan 25;11(1):e0147643. PubMed PMID: 26808658
• Ahn ES, Hauck MJ, Kirk Harris J, Robertson CE, Dailey RA. Bacterial Biofilms in Jones Tubes. Ophthal Plast Reconstr Surg. 2016 Aug 1. [Epub ahead of print] PubMed PMID: 27487729
• Fang R, Wagner BD, Harris JK, Fillon SA. Zero-inflated negative binomial mixed model: an application to two microbial organisms important in oesophagitis. Epidemiol Infect. 2016 Aug;144(11):2447-55. PubMed PMID: 27049299
• Baron JL, Harris JK, Holinger EP, Duda S, Stevens MJ, Robertson CE, Ross KA, Pace NR, Stout JE. Effect of monochloramine treatment on the microbial ecology of Legionella and associated bacterial populations in a hospital hot water system. Syst Appl Microbiol. 2015 May;38(3):198-205. PubMed PMID: 25840824
• Ling AL, Robertson CE, Harris JK, Frank DN, Kotter CV, Stevens MJ, Pace NR, Hernandez MT. High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes. PLoS One. 2015;10(3):e0116400. PubMed PMID: 25748024
• Hull NM, Reens AL, Robertson CE, Stanish LF, Harris JK, Stevens MJ, Frank DN, Kotter C, Pace NR. Molecular analysis of single room humidifier bacteriology. Water Res. 2015 Feb 1;69:318-27. PubMed PMID: 25574772
• Zemanick ET, Wagner BD, Robertson CE, Stevens MJ, Szefler SJ, Accurso FJ, Sagel SD, Harris JK. Assessment of airway microbiota and inflammation in cystic fibrosis using multiple sampling methods. Ann Am Thorac Soc. 2015 Feb;12(2):221-9. PubMed PMID: 25474078
• Keiser NW, Birket SE, Evans IA, Tyler SR, Crooke AK, Sun X, Zhou W, Nellis JR, Stroebele EK, Chu KK, Tearney GJ, Stevens MJ, Harris JK, Rowe SM, Engelhardt JF. Defective innate immunity and hyperinflammation in newborn cystic fibrosis transmembrane conductance regulator-knockout ferret lungs. Am J Respir Cell Mol Biol. 2015 Jun;52(6):683-94. PubMed PMID: 25317669
• Hull NM, Reens AL, Robertson CE, Stanish LF, Harris JK, Stevens MJ, Frank DN, Kotter C, Pace NR. Molecular analysis of single room humidifier bacteriology. Water Res. 2014 Nov 26;69C:318-327. [Epub ahead of print] PubMed PMID: 25574772
• Lim YW, Haynes M, Furlan M, Robertson CE, Harris JK, Rohwer F. Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples. J Vis Exp. 2014 Dec 22;(94). PubMed PMID: 25549184
• Zemanick ET, Wagner BD, Robertson CE, Stevens MJ, Szefler SJ, Accurso FJ, Sagel SD, Harris JK. Assessment of Airway Microbiota and Inflammation in Cystic Fibrosis Using Multiple Sampling Methods. Ann Am Thorac Soc. 2014 Dec 4. [Epub ahead of print] PubMed PMID: 25474078
• Keiser NW, Birket SE, Evans IA, Tyler SR, Crooke AK, Sun X, Zhou W, Nellis JR, Stroebele EK, Chu KK, Tearney GJ, Stevens MJ, Harris JK, Rowe SM, Engelhardt JF. Defective Innate Immunity and Hyper-Inflammation in Newborn CFTR-Knockout Ferret Lungs. Am J Respir Cell Mol Biol. 2014 Oct 15. [Epub ahead of print] PubMed PMID: 25317669
• Ling AL, Robertson CE, Harris JK, Frank DN, Kotter CV, Stevens MJ, Pace NR, Hernandez MT. Carbon dioxide and hydrogen sulfide associations with regional bacterial diversity patterns in microbially induced concrete corrosion. Environ Sci Technol. 2014 Jul 1;48(13):7357-64. PubMed PMID: 24842376
• Whiteson KL, Bailey B, Bergkessel M, Conrad D, Delhaes L, Felts B, Harris JK, Hunter R, Lim YW, Maughan H, Quinn R, Salamon P, Sullivan J, Wagner BD, Rainey PB. The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis. Parallels from island biogeography. Am J Respir Crit Care Med. 2014 Jun 1;189(11):1309-15. PubMed PMID: 24702670
• Holinger EP, Ross KA, Robertson CE, Stevens MJ, Harris JK, Pace NR. Molecular analysis of point-of-use municipal drinking water microbiology. Water Res. 2014 Feb 1;49:225-35. PubMed PMID: 24333849
• Zemanick ET, Harris JK, Wagner BD, Robertson CE, Sagel SD, Stevens MJ, Accurso FJ, Laguna TA. Inflammation and airway microbiota during cystic fibrosis pulmonary exacerbations. PLoS One. 2013;8(4):e62917. PubMed PMID: 23646159
• Robertson CE, Baumgartner LK, Harris JK, Peterson KL, Stevens MJ, Frank DN, Pace NR. Culture-independent analysis of aerosol microbiology in a metropolitan subway system. Appl Environ Microbiol. 2013 Jun;79(11):3485-93. PubMed PMID: 23542619
• Mittal BB, Wang E, Sejpal S, Agulnik M, Mittal A, Harris K. Effect of recombinant human deoxyribonuclease on oropharyngeal secretions in patients with head-and-neck cancers treated with radiochemotherapy. Int J Radiat Oncol Biol Phys. 2013 Oct 1;87(2):282-9. PubMed PMID: 23910712
• Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, Tatem B, Feazel LM, Park K, Pace NR, Frank DN. Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data. Bioinformatics. 2013 Dec 1;29(23):3100-1. PubMed PMID: 24021386
• Goleva E, Jackson LP, Harris JK, Robertson CE, Sutherland ER, Hall CF, Good JT Jr, Gelfand EW, Martin RJ, Leung DY. The effects of airway microbiome on corticosteroid responsiveness in asthma. Am J Respir Crit Care Med. 2013 Nov 15;188(10):1193-201. PubMed PMID: 24024497
• Fillon SA, Harris JK, Wagner BD, Kelly CJ, Stevens MJ, Moore W, Fang R, Schroeder S, Masterson JC, Robertson CE, Pace NR, Ackerman SJ, Furuta GT. Novel device to sample the esophageal microbiome--the esophageal string test. PLoS One. 2012;7(9):e42938. PubMed PMID: 22957025
• Keely S, Kelly CJ, Weissmueller T, Burgess A, Wagner BD, Robertson CE, Harris JK, Colgan SP. Activated fluid transport regulates bacterial-epithelial interactions and significantly shifts the murine colonic microbiome. Gut Microbes. 2012 May-Jun;3(3):250-60. PubMed PMID: 22614705
• Harris JK, Wagner BD. Bacterial identification and analytic challenges in clinical microbiome studies. J Allergy Clin Immunol. 2012 Feb;129(2):441-2. PubMed PMID: 22284932
• El Kasmi KC, Anderson AL, Devereaux MW, Fillon SA, Harris JK, Lovell MA, Finegold MJ, Sokol RJ. Toll-like receptor 4-dependent Kupffer cell activation and liver injury in a novel mouse model of parenteral nutrition and intestinal injury. Hepatology. 2012 May;55(5):1518-28. PubMed PMID: 22120983
• Williamson, KM, Wagner, BD, Robertson, CE, Steven, MJ, Sontag, MK, Mourani, PM and Harris, JK. Modified PCR approach to increase sensitivity for determination of bacterial community composition using high throughput sequencing. BMC Microbiome in press.
• Stanish, LF, Sherwood, O, Lackey, G, Osborn, S, Robertson, CE, Harris, JK and Pace, NR. Microbial and biogeochemical indicators of methane in groundwater aquifers of the Denver Basin, Colorado. Environ. Sci. Technol. In press
• Khalaf, RT, Furuta, GT, Wagner, BD, Robertson, CE, Andrews, R, Stevens, MJ, Fillon, SA, Zemanick, ET and Harris, JK. Influence of acid blockade on the aerodigestive tract microbiome in children with cystic fibrosis. J. Ped. Gastroenterol. Nutr. In press.
• Hoppe, JE, Wagner, BD, Harris, JK, Rowe, SM, Heltshe, SL, DeBoer, EM and Sagel SD. Effects of ivacaftor on systemic inflammation and the plasma proteome in people with CF and G551D. J. Cystic Fibrosis. 2022; in press. PMID: 35440409.
• Furuta GT, Fillon, SA, Williamson, KM, Robertson, CE, Stevens, MJ, Aceves SS, Arva, NC, Chehade, M, Collins, MH, Davis, CM, Dellon, ES, Falk, GW, Gonsalves, N, Gupta, SK, Hirano, I, Khoury, P, Leung, J, Martin, LJ, Menard-Katcher, P, Mukkada, VA, Peterson, K, Spergel, JM, Wechsler, JB, Yang, GY, Rothenberg, ME and Harris, JK. Mucosal microbiota associated with eosinophilic esophagitis and eosinophilic gastritis. J. Ped. Gastroenterol. Nutr. In press.