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Mathematical modelling for antibiotic resistance control policy: do we know enough?

Knight GM, Davies NG, Colijn C, Coll F, Donker T, Gifford DR, Glover RE, Jit M, Klemm E, Lehtinen S, Lindsay JA, Lipsitch M, Llewelyn MJ, Mateus ALP, Robotham JV, Sharland M, Stekel D, Yakob L, Atkins KE.

BMC Infect Dis. 2019 Nov 29;19(1):1011. doi: 10.1186/s12879-019-4630-y.


Depletion-of-susceptibles bias in influenza vaccine waning studies: how to ensure robust results.

Lipsitch M, Goldstein E, Ray GT, Fireman B.

Epidemiol Infect. 2019 Nov 27;147:e306. doi: 10.1017/S0950268819001961.


Surveillance to maintain the sensitivity of genotype-based antibiotic resistance diagnostics.

Hicks AL, Kissler SM, Lipsitch M, Grad YH.

PLoS Biol. 2019 Nov 12;17(11):e3000547. doi: 10.1371/journal.pbio.3000547. eCollection 2019 Nov.


Post-Exposure Effects of Vaccines on Infectious Diseases.

Gallagher T, Lipsitch M.

Epidemiol Rev. 2019 Nov 4. pii: mxz014. doi: 10.1093/epirev/mxz014. [Epub ahead of print]


The Use of Test-negative Controls to Monitor Vaccine Effectiveness: A Systematic Review of Methodology.

Chua H, Feng S, Lewnard JA, Sullivan SG, Blyth CC, Lipsitch M, Cowling BJ.

Epidemiology. 2020 Jan;31(1):43-64. doi: 10.1097/EDE.0000000000001116.


Interaction Patterns of Men Who Have Sex With Men on a Geosocial Networking Mobile App in Seven United States Metropolitan Areas: Observational Study.

Abuelezam NN, Reshef YA, Novak D, Grad YH, Seage Iii GR, Mayer K, Lipsitch M.

J Med Internet Res. 2019 Sep 12;21(9):e13766. doi: 10.2196/13766.


Hospitalizations Associated with Respiratory Syncytial Virus and Influenza in Children, Including Children Diagnosed with Asthma.

Goldstein E, Finelli L, O'Halloran A, Liu P, Karaca Z, Steiner CA, Viboud C, Lipsitch M.

Epidemiology. 2019 Nov;30(6):918-926. doi: 10.1097/EDE.0000000000001092.


Influenza A Hemagglutinin Passage Bias Sites and Host Specificity Mutations.

Lee RTC, Chang HH, Russell CA, Lipsitch M, Maurer-Stroh S.

Cells. 2019 Aug 22;8(9). pii: E958. doi: 10.3390/cells8090958.


Levels of outpatient prescribing for four major antibiotic classes and rates of septicemia hospitalization in adults in different US states - a statistical analysis.

Goldstein E, Olesen SW, Karaca Z, Steiner CA, Viboud C, Lipsitch M.

BMC Public Health. 2019 Aug 19;19(1):1138. doi: 10.1186/s12889-019-7431-8.


Regulating impact on bystanders in clinical trials: An unsettled frontier.

Eyal N, Kimmelman J, Holtzman LG, Lipsitch M.

Clin Trials. 2019 Oct;16(5):450-454. doi: 10.1177/1740774519862783. Epub 2019 Aug 1.


Depletion of Susceptibles Bias in Analyses of Intra-season Waning of Influenza Vaccine Effectiveness.

Ray GT, Lewis N, Klein NP, Daley MF, Lipsitch M, Fireman B.

Clin Infect Dis. 2019 Jul 28. pii: ciz706. doi: 10.1093/cid/ciz706. [Epub ahead of print]


Comment on: 'Antibiotic footprint' as a communication tool to aid reduction of antibiotic consumption.

Lipsitch M, Shaman J.

J Antimicrob Chemother. 2019 Nov 1;74(11):3404-3406. doi: 10.1093/jac/dkz320. No abstract available.


Enhancing Situational Awareness to Prevent Infectious Disease Outbreaks from Becoming Catastrophic.

Lipsitch M, Santillana M.

Curr Top Microbiol Immunol. 2019;424:59-74. doi: 10.1007/82_2019_172.


Resistance diagnostics as a public health tool to combat antibiotic resistance: A model-based evaluation.

McAdams D, Wollein Waldetoft K, Tedijanto C, Lipsitch M, Brown SP.

PLoS Biol. 2019 May 16;17(5):e3000250. doi: 10.1371/journal.pbio.3000250. eCollection 2019 May.


On the evolutionary ecology of multidrug resistance in bacteria.

Lehtinen S, Blanquart F, Lipsitch M, Fraser C; with the Maela Pneumococcal Collaboration.

PLoS Pathog. 2019 May 13;15(5):e1007763. doi: 10.1371/journal.ppat.1007763. eCollection 2019 May.


On the role of different age groups during pertussis epidemics in California, 2010 and 2014.

Mahmud AS, Lipsitch M, Goldstein E.

Epidemiol Infect. 2019 Jan;147:e184. doi: 10.1017/S0950268819000761.


Response to comment on 'The distribution of antibiotic use and its association with antibiotic resistance'.

Olesen SW, Lipsitch M, Grad YH.

Elife. 2019 May 3;8. pii: e47124. doi: 10.7554/eLife.47124.


Modelling the epidemiologic impact of achieving UNAIDS fast-track 90-90-90 and 95-95-95 targets in South Africa.

Abuelezam NN, McCormick AW, Surface ED, Fussell T, Freedberg KA, Lipsitch M, Seage GR.

Epidemiol Infect. 2019 Jan;147:e122. doi: 10.1017/S0950268818003497.


Analysis of a meningococcal meningitis outbreak in Niger - potential effectiveness of reactive prophylaxis.

Hitchings MDT, Coldiron ME, Grais RF, Lipsitch M.

PLoS Negl Trop Dis. 2019 Mar 11;13(3):e0007077. doi: 10.1371/journal.pntd.0007077. eCollection 2019 Mar.


Antimicrobial resistance prevalence, rates of hospitalization with septicemia and rates of mortality with sepsis in adults in different US states.

Goldstein E, MacFadden DR, Karaca Z, Steiner CA, Viboud C, Lipsitch M.

Int J Antimicrob Agents. 2019 Jul;54(1):23-34. doi: 10.1016/j.ijantimicag.2019.03.004. Epub 2019 Mar 6.


Herd immunity alters the conditions for performing dose schedule comparisons: an individual-based model of pneumococcal carriage.

Yang A, Cai F, Lipsitch M.

BMC Infect Dis. 2019 Mar 5;19(1):227. doi: 10.1186/s12879-019-3833-6.


Limited available evidence supports theoretical predictions of reduced vaccine efficacy at higher exposure dose.

Langwig KE, Gomes MGM, Clark MD, Kwitny M, Yamada S, Wargo AR, Lipsitch M.

Sci Rep. 2019 Mar 1;9(1):3203. doi: 10.1038/s41598-019-39698-x.


Population genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13.

Mitchell PK, Azarian T, Croucher NJ, Callendrello A, Thompson CM, Pelton SI, Lipsitch M, Hanage WP.

Microb Genom. 2019 Feb;5(2). doi: 10.1099/mgen.0.000252. Epub 2019 Feb 19.



Lewnard JA, Tedijanto C, Cowling BJ, Lipsitch M.

Am J Epidemiol. 2019 Apr 1;188(4):807-808. doi: 10.1093/aje/kwz018. No abstract available.


Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination.

Campo JJ, Le TQ, Pablo JV, Hung C, Teng AA, Tettelin H, Tate A, Hanage WP, Alderson MR, Liang X, Malley R, Lipsitch M, Croucher NJ.

Elife. 2018 Dec 28;7. pii: e37015. doi: 10.7554/eLife.37015.


The distribution of antibiotic use and its association with antibiotic resistance.

Olesen SW, Barnett ML, MacFadden DR, Brownstein JS, Hernández-Díaz S, Lipsitch M, Grad YH.

Elife. 2018 Dec 18;7. pii: e39435. doi: 10.7554/eLife.39435.


Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora.

Tedijanto C, Olesen SW, Grad YH, Lipsitch M.

Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):E11988-E11995. doi: 10.1073/pnas.1810840115.


Toward economic evaluation of the value of vaccines and other health technologies in addressing AMR.

Sevilla JP, Bloom DE, Cadarette D, Jit M, Lipsitch M.

Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):12911-12919. doi: 10.1073/pnas.1717161115.


Microbiome as a tool and a target in the effort to address antimicrobial resistance.

Relman DA, Lipsitch M.

Proc Natl Acad Sci U S A. 2018 Dec 18;115(51):12902-12910. doi: 10.1073/pnas.1717163115.


Models of immune selection for multi-locus antigenic diversity of pathogens.

Georgieva M, Buckee CO, Lipsitch M.

Nat Rev Immunol. 2019 Jan;19(1):55-62. doi: 10.1038/s41577-018-0092-5. Review.


The Relative Impact of Community and Hospital Antibiotic Use on the Selection of Extended-spectrum Beta-lactamase-producing Escherichia coli.

MacFadden DR, Fisman DN, Hanage WP, Lipsitch M.

Clin Infect Dis. 2019 Jun 18;69(1):182-188. doi: 10.1093/cid/ciy978.


Analyzing Vaccine Trials in Epidemics With Mild and Asymptomatic Infection.

Kahn R, Hitchings M, Wang R, Bellan SE, Lipsitch M.

Am J Epidemiol. 2019 Feb 1;188(2):467-474. doi: 10.1093/aje/kwy239.


Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine.

Cai FY, Fussell T, Cobey S, Lipsitch M.

PLoS Comput Biol. 2018 Oct 1;14(10):e1006333. doi: 10.1371/journal.pcbi.1006333. eCollection 2018 Oct.


Azithromycin Susceptibility Among Neisseria gonorrhoeae Isolates and Seasonal Macrolide Use.

Olesen SW, Torrone EA, Papp JR, Kirkcaldy RD, Lipsitch M, Grad YH.

J Infect Dis. 2019 Jan 29;219(4):619-623. doi: 10.1093/infdis/jiy551.


Challenges of Vaccine Effectiveness and Waning Studies.

Lipsitch M.

Clin Infect Dis. 2019 May 2;68(10):1631-1633. doi: 10.1093/cid/ciy773. No abstract available.


Why Do Exceptionally Dangerous Gain-of-Function Experiments in Influenza?

Lipsitch M.

Methods Mol Biol. 2018;1836:589-608. doi: 10.1007/978-1-4939-8678-1_29. Review.


Measurement of Vaccine Direct Effects Under the Test-Negative Design.

Lewnard JA, Tedijanto C, Cowling BJ, Lipsitch M.

Am J Epidemiol. 2018 Dec 1;187(12):2686-2697. doi: 10.1093/aje/kwy163.


Opinion: Risk to study nonparticipants: A procedural approach.

Eyal N, Lipsitch M, Bärnighausen T, Wikler D.

Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):8051-8053. doi: 10.1073/pnas.1810920115. No abstract available.


Choices in vaccine trial design in epidemics of emerging infections.

Kahn R, Rid A, Smith PG, Eyal N, Lipsitch M.

PLoS Med. 2018 Aug 7;15(8):e1002632. doi: 10.1371/journal.pmed.1002632. eCollection 2018 Aug.


Can antibiotic resistance be reduced by vaccinating against respiratory disease?

Atkins KE, Lipsitch M.

Lancet Respir Med. 2018 Nov;6(11):820-821. doi: 10.1016/S2213-2600(18)30328-X. Epub 2018 Jul 31. No abstract available.


Trends in outpatient antibiotic use and prescribing practice among US older adults, 2011-15: observational study.

Olesen SW, Barnett ML, MacFadden DR, Lipsitch M, Grad YH.

BMJ. 2018 Jul 27;362:k3155. doi: 10.1136/bmj.k3155.


On the Role of Different Age Groups and Pertussis Vaccines During the 2012 Outbreak in Wisconsin.

Goldstein E, Worby CJ, Lipsitch M.

Open Forum Infect Dis. 2018 Apr 16;5(5):ofy082. doi: 10.1093/ofid/ofy082. eCollection 2018 May.


The evolution of antibiotic resistance in a structured host population.

Blanquart F, Lehtinen S, Lipsitch M, Fraser C.

J R Soc Interface. 2018 Jun;15(143). pii: 20180040. doi: 10.1098/rsif.2018.0040.


Impact of Antimicrobial Treatment for Acute Otitis Media on Carriage Dynamics of Penicillin-Susceptible and Penicillin-Nonsusceptible Streptococcus pneumoniae.

Lewnard JA, Tähtinen PA, Laine MK, Lindholm L, Jalava J, Huovinen P, Lipsitch M, Ruohola A.

J Infect Dis. 2018 Sep 22;218(9):1356-1366. doi: 10.1093/infdis/jiy343.


Multidrug-resistant Neisseria gonorrhoeae: implications for future treatment strategies.

MacFadden DR, Lipsitch M, Olesen SW, Grad Y.

Lancet Infect Dis. 2018 Jun;18(6):599. doi: 10.1016/S1473-3099(18)30274-3. No abstract available.


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.


Preprints: An underutilized mechanism to accelerate outbreak science.

Johansson MA, Reich NG, Meyers LA, Lipsitch M.

PLoS Med. 2018 Apr 3;15(4):e1002549. doi: 10.1371/journal.pmed.1002549. eCollection 2018 Apr.


Antigenic Variation in Streptococcus pneumoniae PspC Promotes Immune Escape in the Presence of Variant-Specific Immunity.

Georgieva M, Kagedan L, Lu YJ, Thompson CM, Lipsitch M.

MBio. 2018 Mar 13;9(2). pii: e00264-18. doi: 10.1128/mBio.00264-18.


Competing Effects of Indirect Protection and Clustering on the Power of Cluster-Randomized Controlled Vaccine Trials.

Hitchings MDT, Lipsitch M, Wang R, Bellan SE.

Am J Epidemiol. 2018 Aug 1;187(8):1763-1771. doi: 10.1093/aje/kwy047.


Impact of stochastically generated heterogeneity in hazard rates on individually randomized vaccine efficacy trials.

Kahn R, Hitchings M, Bellan S, Lipsitch M.

Clin Trials. 2018 Apr;15(2):207-211. doi: 10.1177/1740774517752671. Epub 2018 Jan 27.

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