William Hanage

Associate Professor





National Institutes of Health, National Institute of General Medical Sciences
People: Laura White, Ted Cohen, William Hanage, Rene Niehus, Ben Cowling, Tyler Brown, Joseph Wu, Mauricio Santillana Guzman, Joseph Lewnard, Aimee Taylor, Pablo Martinez de Salazar, Lerato Magosi, Edward Goldstein, Christine Tedijanto, Tigist Menkir, Sze Man Leung, Hsiao-Han Chang, Caroline Buckee, Pamela Martinez, Marc Lipsitch
2009 – 2020

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MacFadden DR, Hanage WP. (2019). Potential for Erosion of Efficacy in Noninferiority Trials of Decreasing Duration of Antibiotic Therapy. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 69(7)

Hanage WP. (2019). Two Health or Not Two Health? That Is the Question. MBio, 10(2)

Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP. (2019). Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13. Microbial genomics, 5(2)

Lewnard JA, Hanage WP. (2019). Making sense of differences in pneumococcal serotype replacement. The Lancet. Infectious diseases, 19(6)

Martin MA, Lee RS, Cowley LA, Gardy JL, Hanage WP. (2018). Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission. Microbial genomics, 4(10)

Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP. (2018). Weak Epistasis May Drive Adaptation in Recombining Bacteria. Genetics, 208(3)

MacFadden DR, McGeer A, Athey T, Perusini S, Olsha R, Li A, Eshaghi A, Gubbay JB, Hanage WP. (2018). Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15. Emerging infectious diseases, 24(3)

Azarian T, Mitchell PK, Georgieva M, Thompson CM, Ghouila A, Pollard AJ, von Gottberg A, du Plessis M, Antonio M, Kwambana-Adams BA, Clarke SC, Everett D, Cornick J, Sadowy E, Hryniewicz W, Skoczynska A, Moïsi JC, McGee L, Beall B, Metcalf BJ, Breiman RF, Ho PL, Reid R, O'Brien KL, Gladstone RA, Bentley SD, Hanage WP. (2018). Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci. PLoS pathogens, 14(11)

Hanage WP. (2018). From bacterial genomics to clinical epidemiology: an interview with Bill Hanage. BMC biology, 16(1)

Cowley LA, Petersen FC, Junges R, Jimson D Jimenez M, Morrison DA, Hanage WP. (2018). Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae. PLoS genetics, 14(6)

Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP, Feldgarden M, Chapman SB, Reis-Cunha JL, Shea TP, Young S, Zeng Q, Delaney ML, Kim D, Peterson EM, O'Brien TF, Ferraro MJ, Hooper DC, Huang SS, Kirby JE, Onderdonk AB, Birren BW, Hung DT, Cosimi LA, Wortman JR, Murphy CI, Hanage WP. (2017). Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proceedings of the National Academy of Sciences of the United States of America, 114(5)

Worby CJ, Lipsitch M, Hanage WP. (2017). Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data. American journal of epidemiology, 186(10)

Marttinen P, Hanage WP. (2017). Speciation trajectories in recombining bacterial species. PLoS computational biology, 13(7)

Andam CP, Worby CJ, Gierke R, McGee L, Pilishvili T, Hanage WP. (2017). Penicillin Resistance of Nonvaccine Type Pneumococcus before and after PCV13 Introduction, United States. Emerging infectious diseases, 23(6)

Andam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall BW, Hanage WP. (2017). Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States. Journal of clinical microbiology, 55(4)

Chaguza C, Andam CP, Harris SR, Cornick JE, Yang M, Bricio-Moreno L, Kamng'ona AW, Parkhill J, French N, Heyderman RS, Kadioglu A, Everett DB, Bentley SD, Hanage WP. (2016). Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule. MBio, 7(5)

Hanage WP. (2016). Not So Simple After All: Bacteria, Their Population Genetics, and Recombination. Cold Spring Harbor perspectives in biology, 8(7)

Hausdorff WP, Hanage WP. (2016). Interim results of an ecological experiment - Conjugate vaccination against the pneumococcus and serotype replacement. Human vaccines & immunotherapeutics, 12(2)

Chang Q, Lipsitch M, Hanage WP. (2016). Impact of Host Heterogeneity on the Efficacy of Interventions to Reduce Staphylococcus aureus Carriage. Infection control and hospital epidemiology, 37(2)

Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WP. (2015). Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae. Scientific data

Chang Q, Stevenson AE, Croucher NJ, Lee GM, Pelton SI, Lipsitch M, Finkelstein JA, Hanage WP. (2015). Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced. BMC infectious diseases

Mitchell PK, Lipsitch M, Hanage WP. (2015). Carriage burden, multiple colonization and antibiotic pressure promote emergence of resistant vaccine escape pneumococci. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 370(1670)

Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP. (2015). Selective and genetic constraints on pneumococcal serotype switching. PLoS genetics, 11(3)

Marttinen P, Croucher NJ, Gutmann MU, Corander J, Hanage WP. (2015). Recombination produces coherent bacterial species clusters in both core and accessory genomes. Microbial genomics, 1(5)

Andam CP, Hanage WP. (2015). Mechanisms of genome evolution of Streptococcus. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

Chang Q, Wang W, Regev-Yochay G, Lipsitch M, Hanage WP. (2015). Antibiotics in agriculture and the risk to human health: how worried should we be?. Evolutionary applications, 8(3)

Hanage WP. (2014). Microbiology: Microbiome science needs a healthy dose of scepticism. Nature, 512(7514)

Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP. (2014). Diversification of bacterial genome content through distinct mechanisms over different timescales. Nature communications

Worby CJ, Lipsitch M, Hanage WP. (2014). Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS computational biology, 10(3)

Grad YH, Godfrey P, Cerquiera GC, Mariani-Kurkdjian P, Gouali M, Bingen E, Shea TP, Haas BJ, Griggs A, Young S, Zeng Q, Lipsitch M, Waldor MK, Weill FX, Wortman JR, Hanage WP. (2013). Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen. MBio, 4(1)

Croucher NJ, Harris SR, Grad YH, Hanage WP. (2013). Bacterial genomes in epidemiology--present and future. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 368(1614)

Hanage WP. (2013). Fuzzy species revisited. BMC biology

Shepheard MA, Fleming VM, Connor TR, Corander J, Feil EJ, Fraser C, Hanage WP. (2013). Historical zoonoses and other changes in host tropism of Staphylococcus aureus, identified by phylogenetic analysis of a population dataset. PLoS One, 8(5)

Polz MF, Alm EJ, Hanage WP. (2013). Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends in genetics : TIG, 29(3)

Grad YH, Lipsitch M, Griggs AD, Haas BJ, Shea TP, McCowan C, Montmayeur A, FitzGerald M, Wortman JR, Krogfelt KA, Bingen E, Weill FX, Tietze E, Flieger A, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP. (2012). Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany. Proceedings of the National Academy of Sciences of the United States of America, 109(52)

Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Møller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP. (2012). Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proceedings of the National Academy of Sciences of the United States of America, 109(8)

Corander J, Connor TR, O'Dwyer CA, Kroll JS, Hanage WP. (2012). Population structure in the Neisseria, and the biological significance of fuzzy species. Journal of the Royal Society, Interface, 9(71)

Connor TR, Corander J, Hanage WP. (2012). Population subdivision and the detection of recombination in non-typable Haemophilus influenzae. Microbiology (Reading, England), 158(Pt 12)

Scott JR, Hinds J, Gould KA, Millar EV, Reid R, Santosham M, O'Brien KL, Hanage WP. (2012). Nontypeable pneumococcal isolates among navajo and white mountain apache communities: are these really a cause of invasive disease?. The Journal of infectious diseases, 206(1)

Hanage WP, Bishop CJ, Huang SS, Stevenson AE, Pelton SI, Lipsitch M, Finkelstein JA. (2011). Carried pneumococci in Massachusetts children: the contribution of clonal expansion and serotype switching. The Pediatric infectious disease journal, 30(4)

Hanage WP, Finkelstein JA, Huang SS, Pelton SI, Stevenson AE, Kleinman K, Hinrichsen VL, Fraser C. (2010). Evidence that pneumococcal serotype replacement in Massachusetts following conjugate vaccination is now complete. Epidemics, 2(2)

Hanage WP, Fraser C, Tang J, Connor TR, Corander J. (2009). Hyper-recombination, diversity, and antibiotic resistance in pneumococcus. Science (New York, N.Y.), 324(5933)

Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. (2009). The bacterial species challenge: making sense of genetic and ecological diversity. Science (New York, N.Y.), 323(5915)

Hanage WP, Aanensen DM. (2009). Methods for data analysis. Methods in molecular biology (Clifton, N.J.)

Hanage WP. (2008). Serotype-specific problems associated with pneumococcal conjugate vaccination. Future microbiology, 3(1)

Fraser C, Hollingsworth TD, Chapman R, de Wolf F, Hanage WP. (2007). Variation in HIV-1 set-point viral load: epidemiological analysis and an evolutionary hypothesis. Proceedings of the National Academy of Sciences of the United States of America, 104(44)

Pelton SI, Huot H, Finkelstein JA, Bishop CJ, Hsu KK, Kellenberg J, Huang SS, Goldstein R, Hanage WP. (2007). Emergence of 19A as virulent and multidrug resistant Pneumococcus in Massachusetts following universal immunization of infants with pneumococcal conjugate vaccine. The Pediatric infectious disease journal, 26(6)

Hanage WP, Huang SS, Lipsitch M, Bishop CJ, Godoy D, Pelton SI, Goldstein R, Huot H, Finkelstein JA. (2007). Diversity and antibiotic resistance among nonvaccine serotypes of Streptococcus pneumoniae carriage isolates in the post-heptavalent conjugate vaccine era. The Journal of infectious diseases, 195(3)

Hanage WP, Fraser C, Spratt BG. (2006). Sequences, sequence clusters and bacterial species. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 361(1475)

Hanage WP, Spratt BG, Turner KM, Fraser C. (2006). Modelling bacterial speciation. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 361(1475)

Hanage WP, Fraser C, Spratt BG. (2006). The impact of homologous recombination on the generation of diversity in bacteria. Journal of theoretical biology, 239(2)

Hanage WP, Fraser C, Spratt BG. (2005). Fuzzy species among recombinogenic bacteria. BMC biology

Hanage WP, Kaijalainen T, Herva E, Saukkoriipi A, Syrjänen R, Spratt BG. (2005). Using multilocus sequence data to define the pneumococcus. Journal of bacteriology, 187(17)

Hanage WP, Kaijalainen TH, Syrjänen RK, Auranen K, Leinonen M, Mäkelä PH, Spratt BG. (2005). Invasiveness of serotypes and clones of Streptococcus pneumoniae among children in Finland. Infection and immunity, 73(1)

Hanage WP, Auranen K, Syrjänen R, Herva E, Mäkelä PH, Kilpi T, Spratt BG. (2004). Ability of pneumococcal serotypes and clones to cause acute otitis media: implications for the prevention of otitis media by conjugate vaccines. Infection and immunity, 72(1)