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Items: 1 to 50 of 117

1.

Genomic epidemiology of meticillin-resistant Staphylococcus aureus ST22 widespread in communities of the Gaza Strip, 2009.

Chang Q, Abuelaish I, Biber A, Jaber H, Callendrello A, Andam CP, Regev-Yochay G, Hanage WP, On Behalf Of The Picr Study Group.

Euro Surveill. 2018 Aug;23(34). doi: 10.2807/1560-7917.ES.2018.23.34.1700592.

2.

Evolution via recombination: Cell-to-cell contact facilitates larger recombination events in Streptococcus pneumoniae.

Cowley LA, Petersen FC, Junges R, Jimson D Jimenez M, Morrison DA, Hanage WP.

PLoS Genet. 2018 Jun 13;14(6):e1007410. doi: 10.1371/journal.pgen.1007410. eCollection 2018 Jun.

3.

The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.

Azarian T, Grant LR, Arnold BJ, Hammitt LL, Reid R, Santosham M, Weatherholtz R, Goklish N, Thompson CM, Bentley SD, O'Brien KL, Hanage WP, Lipsitch M.

PLoS Pathog. 2018 Apr 4;14(4):e1006966. doi: 10.1371/journal.ppat.1006966. eCollection 2018 Apr.

4.

Use of Genome Sequencing to Define Institutional Influenza Outbreaks, Toronto, Ontario, Canada, 2014-15.

MacFadden DR, McGeer A, Athey T, Perusini S, Olsha R, Li A, Eshaghi A, Gubbay JB, Hanage WP.

Emerg Infect Dis. 2018 Mar;24(3):492-497. doi: 10.3201/eid2403.171499.

5.

Weak Epistasis May Drive Adaptation in Recombining Bacteria.

Arnold BJ, Gutmann MU, Grad YH, Sheppard SK, Corander J, Lipsitch M, Hanage WP.

Genetics. 2018 Mar;208(3):1247-1260. doi: 10.1534/genetics.117.300662. Epub 2018 Jan 12.

PMID:
29330348
6.

Shared Genomic Variants: Identification of Transmission Routes Using Pathogen Deep-Sequence Data.

Worby CJ, Lipsitch M, Hanage WP.

Am J Epidemiol. 2017 Nov 15;186(10):1209-1216. doi: 10.1093/aje/kwx182.

7.

Frequency-dependent selection in vaccine-associated pneumococcal population dynamics.

Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP, Bentley SD, Lipsitch M, Croucher NJ.

Nat Ecol Evol. 2017 Dec;1(12):1950-1960. doi: 10.1038/s41559-017-0337-x. Epub 2017 Oct 16.

8.

Immunization, Antibiotic Use, and Pneumococcal Colonization Over a 15-Year Period.

Lee GM, Kleinman K, Pelton S, Lipsitch M, Huang SS, Lakoma M, Dutta-Linn M, Rett M, Hanage WP, Finkelstein JA.

Pediatrics. 2017 Nov;140(5). pii: e20170001. doi: 10.1542/peds.2017-0001. Epub 2017 Oct 4.

PMID:
28978716
9.

Population genetic structure, antibiotic resistance, capsule switching and evolution of invasive pneumococci before conjugate vaccination in Malawi.

Chaguza C, Cornick JE, Andam CP, Gladstone RA, Alaerts M, Musicha P, Peno C, Bar-Zeev N, Kamng'ona AW, Kiran AM, Msefula CL, McGee L, Breiman RF, Kadioglu A, French N, Heyderman RS, Hanage WP, Bentley SD, Everett DB.

Vaccine. 2017 Aug 16;35(35 Pt B):4594-4602. doi: 10.1016/j.vaccine.2017.07.009. Epub 2017 Jul 12.

10.

Speciation trajectories in recombining bacterial species.

Marttinen P, Hanage WP.

PLoS Comput Biol. 2017 Jul 3;13(7):e1005640. doi: 10.1371/journal.pcbi.1005640. eCollection 2017 Jul.

11.

Surveillance of pneumococcal colonization and invasive pneumococcal disease reveals shift in prevalent carriage serotypes in Massachusetts' children to relatively low invasiveness.

Yildirim I, Little BA, Finkelstein J, Lee G, Hanage WP, Shea K, Pelton SI; T; he Massachusetts Dept. of Public Health.

Vaccine. 2017 Jul 13;35(32):4002-4009. doi: 10.1016/j.vaccine.2017.05.077. Epub 2017 Jun 20.

PMID:
28645717
12.

Penicillin Resistance of Nonvaccine Type Pneumococcus before and after PCV13 Introduction, United States.

Andam CP, Worby CJ, Gierke R, McGee L, Pilishvili T, Hanage WP.

Emerg Infect Dis. 2017 Jun;23(6):1012-1015. doi: 10.3201/eid2306.161331.

13.

Efficient Inference of Recent and Ancestral Recombination within Bacterial Populations.

Mostowy R, Croucher NJ, Andam CP, Corander J, Hanage WP, Marttinen P.

Mol Biol Evol. 2017 May 1;34(5):1167-1182. doi: 10.1093/molbev/msx066.

14.

Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States.

Andam CP, Mitchell PK, Callendrello A, Chang Q, Corander J, Chaguza C, McGee L, Beall BW, Hanage WP.

J Clin Microbiol. 2017 Apr;55(4):1104-1115. doi: 10.1128/JCM.02453-16. Epub 2017 Jan 18.

15.

Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks.

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.

Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1135-1140. doi: 10.1073/pnas.1616248114. Epub 2017 Jan 17.

16.

Diverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening.

Croucher NJ, Campo JJ, Le TQ, Liang X, Bentley SD, Hanage WP, Lipsitch M.

Proc Natl Acad Sci U S A. 2017 Jan 17;114(3):E357-E366. doi: 10.1073/pnas.1613937114. Epub 2017 Jan 4.

17.

Association of Pneumococcal Protein Antigen Serology With Age and Antigenic Profile of Colonizing Isolates.

Azarian T, Grant LR, Georgieva M, Hammitt LL, Reid R, Bentley SD, Goldblatt D, Santosham M, Weatherholtz R, Burbidge P, Goklish N, Thompson CM, Hanage WP, O'Brien KL, Lipsitch M.

J Infect Dis. 2017 Mar 1;215(5):713-722. doi: 10.1093/infdis/jiw628.

18.

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms.

Harms K, Lunnan A, Hülter N, Mourier T, Vinner L, Andam CP, Marttinen P, Fridholm H, Hansen AJ, Hanage WP, Nielsen KM, Willerslev E, Johnsen PJ.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15066-15071. doi: 10.1073/pnas.1615819114. Epub 2016 Dec 12.

19.

Understanding pneumococcal serotype 1 biology through population genomic analysis.

Chaguza C, Cornick JE, Harris SR, Andam CP, Bricio-Moreno L, Yang M, Yalcin F, Ousmane S, Govindpersad S, Senghore M, Ebruke C, Du Plessis M, Kiran AM, Pluschke G, Sigauque B, McGee L, Klugman KP, Turner P, Corander J, Parkhill J, Collard JM, Antonio M, von Gottberg A, Heyderman RS, French N, Kadioglu A, Hanage WP, Everett DB, Bentley SD; PAGe Consortium.

BMC Infect Dis. 2016 Nov 8;16(1):649.

20.

Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule.

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.

MBio. 2016 Sep 27;7(5). pii: e01053-16. doi: 10.1128/mBio.01053-16.

21.

Intrahost Evolution of Methicillin-Resistant Staphylococcus aureus USA300 Among Individuals With Reoccurring Skin and Soft-Tissue Infections.

Azarian T, Daum RS, Petty LA, Steinbeck JL, Yin Z, Nolan D, Boyle-Vavra S, Hanage WP, Salemi M, David MZ.

J Infect Dis. 2016 Sep 15;214(6):895-905. doi: 10.1093/infdis/jiw242. Epub 2016 Jun 10.

22.

Not So Simple After All: Bacteria, Their Population Genetics, and Recombination.

Hanage WP.

Cold Spring Harb Perspect Biol. 2016 Jul 1;8(7). pii: a018069. doi: 10.1101/cshperspect.a018069. Review.

23.

The impact of host metapopulation structure on the population genetics of colonizing bacteria.

Numminen E, Gutmann M, Shubin M, Marttinen P, Méric G, van Schaik W, Coque TM, Baquero F, Willems RJ, Sheppard SK, Feil EJ, Hanage WP, Corander J.

J Theor Biol. 2016 May 7;396:53-62. doi: 10.1016/j.jtbi.2016.02.019. Epub 2016 Feb 23.

PMID:
26916623
24.

Interim results of an ecological experiment - Conjugate vaccination against the pneumococcus and serotype replacement.

Hausdorff WP, Hanage WP.

Hum Vaccin Immunother. 2016;12(2):358-74. doi: 10.1080/21645515.2015.1118593. Review. Erratum in: Hum Vaccin Immunother. 2016 Sep;12 (9):2478-81.

25.

Identifying the effect of patient sharing on between-hospital genetic differentiation of methicillin-resistant Staphylococcus aureus.

Chang HH, Dordel J, Donker T, Worby CJ, Feil EJ, Hanage WP, Bentley SD, Huang SS, Lipsitch M.

Genome Med. 2016 Feb 13;8(1):18. doi: 10.1186/s13073-016-0274-3.

26.

Impact of Host Heterogeneity on the Efficacy of Interventions to Reduce Staphylococcus aureus Carriage.

Chang Q, Lipsitch M, Hanage WP.

Infect Control Hosp Epidemiol. 2016 Feb;37(2):197-204. doi: 10.1017/ice.2015.269. Epub 2015 Nov 24. Erratum in: Infect Control Hosp Epidemiol. 2016 Feb;37(2):244.

27.

Recombination produces coherent bacterial species clusters in both core and accessory genomes.

Marttinen P, Croucher NJ, Gutmann MU, Corander J, Hanage WP.

Microb Genom. 2015 Nov 5;1(5):e000038. doi: 10.1099/mgen.0.000038. eCollection 2015 Nov.

28.

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.

Croucher NJ, Finkelstein JA, Pelton SI, Parkhill J, Bentley SD, Lipsitch M, Hanage WP.

Sci Data. 2015 Oct 27;2:150058. doi: 10.1038/sdata.2015.58. eCollection 2015.

29.

Estimating the hospitalization burden associated with influenza and respiratory syncytial virus in New York City, 2003-2011.

Goldstein E, Greene SK, Olson DR, Hanage WP, Lipsitch M.

Influenza Other Respir Viruses. 2015 Sep;9(5):225-33. doi: 10.1111/irv.12325.

30.

Identification of pneumococcal colonization determinants in the stringent response pathway facilitated by genomic diversity.

Li Y, Croucher NJ, Thompson CM, Trzciński K, Hanage WP, Lipsitch M.

BMC Genomics. 2015 May 9;16:369. doi: 10.1186/s12864-015-1573-6.

31.

Carriage burden, multiple colonization and antibiotic pressure promote emergence of resistant vaccine escape pneumococci.

Mitchell PK, Lipsitch M, Hanage WP.

Philos Trans R Soc Lond B Biol Sci. 2015 Jun 5;370(1670):20140342. doi: 10.1098/rstb.2014.0342.

32.

Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis.

Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MC, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK.

Genome Biol Evol. 2015 Apr 16;7(5):1313-28. doi: 10.1093/gbe/evv066.

33.

Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157.

Dallman TJ, Byrne L, Ashton PM, Cowley LA, Perry NT, Adak G, Petrovska L, Ellis RJ, Elson R, Underwood A, Green J, Hanage WP, Jenkins C, Grant K, Wain J.

Clin Infect Dis. 2015 Aug 1;61(3):305-12. doi: 10.1093/cid/civ318. Epub 2015 Apr 17.

34.

Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced.

Chang Q, Stevenson AE, Croucher NJ, Lee GM, Pelton SI, Lipsitch M, Finkelstein JA, Hanage WP.

BMC Infect Dis. 2015 Feb 18;15:68. doi: 10.1186/s12879-015-0797-z.

35.

Antibiotics in agriculture and the risk to human health: how worried should we be?

Chang Q, Wang W, Regev-Yochay G, Lipsitch M, Hanage WP.

Evol Appl. 2015 Mar;8(3):240-7. doi: 10.1111/eva.12185. Epub 2014 Aug 2. Review.

36.

Selective and genetic constraints on pneumococcal serotype switching.

Croucher NJ, Kagedan L, Thompson CM, Parkhill J, Bentley SD, Finkelstein JA, Lipsitch M, Hanage WP.

PLoS Genet. 2015 Mar 31;11(3):e1005095. doi: 10.1371/journal.pgen.1005095. eCollection 2015 Mar.

37.

Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics.

Perron GG, Whyte L, Turnbaugh PJ, Goordial J, Hanage WP, Dantas G, Desai MM.

PLoS One. 2015 Mar 25;10(3):e0069533. doi: 10.1371/journal.pone.0069533. eCollection 2015.

38.

Origin and proliferation of multiple-drug resistance in bacterial pathogens.

Chang HH, Cohen T, Grad YH, Hanage WP, O'Brien TF, Lipsitch M.

Microbiol Mol Biol Rev. 2015 Mar;79(1):101-16. doi: 10.1128/MMBR.00039-14. Review.

39.

Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.

Hilty M, Wüthrich D, Salter SJ, Engel H, Campbell S, Sá-Leão R, de Lencastre H, Hermans P, Sadowy E, Turner P, Chewapreecha C, Diggle M, Pluschke G, McGee L, Köseoğlu Eser Ö, Low DE, Smith-Vaughan H, Endimiani A, Küffer M, Dupasquier M, Beaudoing E, Weber J, Bruggmann R, Hanage WP, Parkhill J, Hathaway LJ, Mühlemann K, Bentley SD.

Genome Biol Evol. 2014 Dec 4;6(12):3281-94. doi: 10.1093/gbe/evu263.

40.

Mechanisms of genome evolution of Streptococcus.

Andam CP, Hanage WP.

Infect Genet Evol. 2015 Jul;33:334-42. doi: 10.1016/j.meegid.2014.11.007. Epub 2014 Nov 13. Review.

41.

Diversification of bacterial genome content through distinct mechanisms over different timescales.

Croucher NJ, Coupland PG, Stevenson AE, Callendrello A, Bentley SD, Hanage WP.

Nat Commun. 2014 Nov 19;5:5471. doi: 10.1038/ncomms6471.

42.

The distribution of pairwise genetic distances: a tool for investigating disease transmission.

Worby CJ, Chang HH, Hanage WP, Lipsitch M.

Genetics. 2014 Dec;198(4):1395-404. doi: 10.1534/genetics.114.171538. Epub 2014 Oct 13.

43.

Microbiology: Microbiome science needs a healthy dose of scepticism.

Hanage WP.

Nature. 2014 Aug 21;512(7514):247-8. doi: 10.1038/512247a. No abstract available.

PMID:
25143098
44.

Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes.

Chewapreecha C, Marttinen P, Croucher NJ, Salter SJ, Harris SR, Mather AE, Hanage WP, Goldblatt D, Nosten FH, Turner C, Turner P, Bentley SD, Parkhill J.

PLoS Genet. 2014 Aug 7;10(8):e1004547. doi: 10.1371/journal.pgen.1004547. eCollection 2014 Aug.

45.

Biomedical Ph.D. students enrolled in two elite universities in the United kingdom and the United States report adopting multiple learning relationships.

Kemp MW, Lazarus BM, Perron GG, Hanage WP, Chapman E.

PLoS One. 2014 Jul 23;9(7):e103075. doi: 10.1371/journal.pone.0103075. eCollection 2014.

46.

Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone.

Croucher NJ, Hanage WP, Harris SR, McGee L, van der Linden M, de Lencastre H, Sá-Leão R, Song JH, Ko KS, Beall B, Klugman KP, Parkhill J, Tomasz A, Kristinsson KG, Bentley SD.

BMC Biol. 2014 Jun 23;12:49. doi: 10.1186/1741-7007-12-49.

47.

Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape.

Croucher NJ, Chewapreecha C, Hanage WP, Harris SR, McGee L, van der Linden M, Song JH, Ko KS, de Lencastre H, Turner C, Yang F, Sá-Leão R, Beall B, Klugman KP, Parkhill J, Turner P, Bentley SD.

Genome Biol Evol. 2014 Jun 10;6(7):1589-602. doi: 10.1093/gbe/evu120.

48.

Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution.

Mostowy R, Croucher NJ, Hanage WP, Harris SR, Bentley S, Fraser C.

PLoS Genet. 2014 May 1;10(5):e1004300. doi: 10.1371/journal.pgen.1004300. eCollection 2014 May.

49.

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals.

Sheppard SK, Cheng L, Méric G, de Haan CP, Llarena AK, Marttinen P, Vidal A, Ridley A, Clifton-Hadley F, Connor TR, Strachan NJ, Forbes K, Colles FM, Jolley KA, Bentley SD, Maiden MC, Hänninen ML, Parkhill J, Hanage WP, Corander J.

Mol Ecol. 2014 May;23(10):2442-51. doi: 10.1111/mec.12742. Epub 2014 Apr 25.

50.

Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data.

Worby CJ, Lipsitch M, Hanage WP.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003549. doi: 10.1371/journal.pcbi.1003549. eCollection 2014 Mar.

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