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Associate Investigator Microbial Genomics Section

Translational and Functional Genomics Branch


B.S. Florida State University, 1996

Ph.D. Texas A&M University, 2003


Dr. Sean Conlan is an associate investigator in the Microbial Genomics Section (MGS) of the Translational and Functional Genomics Branch at NHGRI. He earned his bachelors in Biochemistry from Florida State University in 1996. In 2003 he earned his Ph.D. in medical biochemistry from Texas A&M University studying bacterial membrane proteins in the laboratory of Dr. Hagan Bayley. He conducted postdoctoral research from 2003 to 2006 at The Wadsworth Center, New York State Department of Health, where he used motif finding algorithms to identify bacterial regulatory networks. From 2006 to 2008, he developed computational tools for detecting pathogens in clinical samples as part of the Center for Infection and Immunity at Columbia University. He's been a staff scientist in Julie Segre's group since 2008.

Dr. Conlan oversees bioinformatics for the MGS and splits his time between data management responsibilities and basic research. The MGS uses a variety of DNA sequencing strategies and platforms to answer basic research questions on a) the human skin microbiome and b) hospital associated pathogens. Dr. Conlan works closely with the NIH Intramural Sequencing Center to process, analyze and publicly deposit sequencing data associated with MGS projects. He also does basic research on the mechanisms of antibiotic resistance, plasmid biology and molecular epidemiology of hospital associated pathogens.

Scientific Summary

Dr. Conlan is interested in scientific problems that lie at the intersection of biology and bioinformatics. As part of the Microbial Genomics Section (MGS), Dr. Conlan applies cutting edge sequencing and analysis to problems associated with hospital-acquired infections, in particular carbapenem-resistant Enterobacteriaceae (CRE). CRE are formidable gram-negative bacterial pathogens that pose a serious threat to hospitalized patients around the globe. CRE are resistant to most, if not all, antibiotics, with investigations reporting as high as a 40 to 80 percent mortality rate from infection.

A common feature of CRE is that genes encoding resistance to antibiotics are carried on mobile DNA sequences called plasmids that can be shared between distantly related bacteria. The MGS uses both Illumina short-read sequencing and PacBio long-read sequencing to characterize isolates from patients and the environment. Dr. Conlan uses these data to compare bacterial isolates, identify epidemiological connections and identify clinically important plasmids. He is particularly interested in identifying genomic features that connect patients to each other or to the environment.


Byrd AL, Deming C, Cassidy S, Harrison OJ, Conlans S, NISC Comparative Sequencing Program, Belkaid Y, Segre JA and Kong HH. Staphylococcal strain diversity modulates atopic dermatitis disease pathogenesis. [In Press]

Dekker BK, Lau AF, Dekker JP, Spalding CD, Sinaii N, Conlan S, Dodd LE, Henderson DK, Segre JA, Frank KM and Palmore TN. Perirectal colonization of healthcare personnel with multidrug resistant organisms. [In Press]

Chen M, Conlan S, Lau AF, Deming C, NISC Comparative Sequencing Program, Frank KM, Palmore TN and Segre JA. Whole genome sequencing overrules a suspected case of carbapenem-resistant Enterobacter cloacae transmission. [InPress]

Hardiman CA, Weingarten RA, Conlan S, Khil P, Dekker JP, Mathers AJ, Sheppard AE, Palmore TN, Segre JA and Frank KM. Horizontal transfer of carbapenemase-encoding plasmids and comparison with hospital epidemiology data. Antimicrob Agents Chemother,60(8)4910-9. 2016. [PubMed]

Conlan S, Lau AF, NISC Comparative Sequencing Program, Palmore TN, Frank KM and Segre JA. Complete genome sequence of a Klebsiella pneumoniae carrying blaNDM-1 on a multidrug resistance plasmid. GenomeA, 4(4):e00664-16. 2016. [PubMed]

Conlan S, Park M, Deming C, Thomas PJ, Young AC, Coleman H, Sison C, NISC Comparative Sequencing Program, Weingarten RA, Lau AF, Dekker JP, Palmore TN, Frank KM and Segre JA. Plasmid dynamics in KPC-Positive Klebsiella pneumoniae during long-term patient colonization. MBio, 7(3):e00742-16. 2016. [PubMed]

Jo J-H, Deming C, Kennedy EA, Conlan S, Polley EC, Ng W-I, NISC Comparative Sequencing Program, Segre JA and Kong HH. Diverse human skin fungal communities in children converge in adulthood.J Invest Dermatol, 136(12):2356-2363. 2016. [PubMed]

Hughes HY, Conlan SP, Lau AF, Dekker JP, Michelin AV, Youn JH, Henderson DK, Frank KM, Segre JA and Palmore TN. Detection and whole genome sequencing of carbapenemase-producing Aeromonas hydrophila from routine perirectal surveillance culture. JCM, 54(4):1167-70. 2016. [PubMed]

Tsai Y-C, Conlan S, Deming C, NISC Comparative Sequencing Program, Segre JA, Kong HH, Korlach J and Oh J. Resolving the complexity of human skin metagenomes using single molecule sequencing. MBio, 7(1):e01948-15. 2016. [PubMed]

Dotson GA, NISC Comparative Sequencing Program, Dekker JP, Palmore TN, Segre JA and Conlan S. Draft Genome Sequence of a KPC+ Sequence Type 111 Pseudomonas aeruginosa. GenomeA, 4(1):e01663-15. 2016. [PubMed]

Naik S, Bouladoux N, Linehan JL, Han S, Harrison OJ, Wilhelm C, Conlan S, Himmelfarb S, Byrd AL, Deming C, Quinones M, Brenchley JM, Kong HH, Tussiwand R, Murphy KM, Merad M, Segre JA and Belkaid Y. Commensal-dendritic-cell interaction specifies a unique protective skin immune signature. Nature, 520(7545):104-8. 2015. [PubMed]

Conlan S, Deming C, Tsai Y-C, Lau AF, Dekker JP, Korlach J and Segre JA. Complete Genome Sequence of a Klebsiella pneumoniaewith Chromosomally Encoded Carbapenem Resistance and Colibactin Synthesis Loci. Genome A, 2(6):e01332-14. 2014. [PubMed]

Oh J, Bryd AL, Deming C, Conlan S, NISC Comparative Sequencing Program, Kong HH and Segre JA. The biogeography of the human skin metagenome reveals novel functional divergence defined by skin habitat and individual variation. Nature, 513(7520):59-64. 2014. [PubMed]

Conlan S, Thomas PJ, Deming C, Deming C, Park M, Lau AF, Dekker JP, Snitkin ES, Clark TA, Luong K, Song Y, Tsai Y-C, Boitano M, Dayal J, Brooks SY, Schmidt B, Young AC, Thomas JW, Bouffard GG, Blakesley RW, NISC Comparative Sequencing Program, Mullikin JC, Korlach J, Henderson DK, Frank KM, Palmore TN and Segre JA. Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae. Science Translational Medicine 6(254), 254ra126. 2014. [PubMed]

van Duin D, Perez F, Rudin SD, Cober E, Hanrahan J, Ziegler J, Webber R, Fox J, Mason P, Richter SS, Cline M, Hall GS, Kaye KS, Jacobs MR, Kalayjian RC, Salata RA, Segre JA, Conlan S, Evans S, Fowler VG and Bonomo RA. Surveillance of Carbapenem-Resistant Klebsiella pneumoniae: Tracking Molecular Epidemiology and Outcomes through a Regional Network. Antimicrob Agents Chemother,58(7):4035-4041. 2014. [PubMed]

Curtis DS, Phillips AR, Callister SJ, Conlan S and McCue LA. SPOCS: software for predicting and visualizing orthology/paralogy relationships among bacterial genomes. Bioinformatics 29(20), 2641-42. 2013. [PubMed]

Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M, NISC Comparative Sequencing Program, Kong HH, and Segre JA. Human skin fungal diversity. Nature, 498(7454):367-70. 2013. [PubMed]

Zelazny AM, Ding L, Goldberg JB, Mijares L, Conlan S, Conville PS, Stock F, Ballentine SJ, Olivier KN, Sampaio EP, Murray PR and Holland SM. Adaptability and persistence of the emerging pathogen Bordetella petrii. PLoS One, 8(6): e65102. 2013. [PubMed]

Conlan S, Kong HH and Segre JA. Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project. PLoS One,7(10):e47075. 2012. [PubMed]

Oh J, Conlan S, Polley E, Segre JA and Kong HH. Shifts in human skin and nares microbiota of healthy children and adults. Genome Med, 4(10):77. 2012. [PubMed]

Naik S, Bouladoux N, Salcedo R, Kastenmuller W, Deming C, Quinones M, Brown C, Koo L, Conlan S, Spencer S, Hall J, Dzutsev A, Trinchierir G, Segre JA and Belkaid Y. Compartmentalized control of skin immunity by resident commensals. Science, 337(6098):1115-9. 2012. [PubMed]

Conlan S, Mijares LA, NISC Comparative Sequence Program, Becker J, Blakesley RR, Bouffard GG, Brooks S, Gupta J, Gurson N, ParkM, Schmidt B, Thomas PJ, Young A, Otto M, Kong HH, Murray PR and Segre JA. Staphylococcus epidermidis pan-genome sequence analysis reveals diversity of skin commensal and hospital infection-associated isolates. Genome Biology, 13(7):R64. 2012. [PubMed]

The Human Microbiome Consortium. Structure, Function and Diversity of the Human Microbiome in an Adult Reference Population. Nature, 486(7402):207-14. 2012. [PubMed]

The Human Microbiome Consortium. A Framework for Human Microbiome Research. Nature, 486(7402):215-21. 2012. [PubMed]

Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley E, Komarow HD, NISC Comparative Sequence Program, Murray PR, Turner ML and Segre JA. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Research, 22(5):850-9. 2012). [PubMed]

Last updated: December 8, 2016