Mathematical assessment of the impact of cohort vaccination on pneumococcal carriage and serotype replacement

References

• E.M.C. D'Agata, G.F. Webb, and J. Pressley, Rapid emergence of co-colonization with community-acquired and hospital-acquired methicillin-resistant staphylococcus aureus strains in the hospital setting, Math. Model. Nat. Phenom. 5(3), pp. 76–93.
   PubMed Web of Science ®Google Scholar
• R. Austrian, Some aspects of the pnuemococcal carrier state, J. Antimicrob. Chemother. 18(Suppl A) (1986), pp. 35–45.
   PubMed Web of Science ®Google Scholar
• R.M. Anderson and R.M. May, Infectious Diseases of Humans, Oxford University Press, New York, 1991.
   Google Scholar
• K. Atkins, E.I. Lafferty, S.R. Deeny, N.G. Davies, J.V. Robotham, and M. Jit, Use of mathematical modelling to assess the impact of vaccines on antibiotic resistance, Lancet Infect. Dis. 18 (2018), pp. e204–13.
   PubMed Web of Science ®Google Scholar
• K. Auranen, J. Mehtala, A. Tanskanen, and M.S. Kaltoft, Between-strain competition in acquisition and clearance of pneumococcal carriage: Epidemiologic evidence from a longitudinal study of day-care children, Am. J. Epidemiol. 171(2) (2010), pp. 169–176.
   PubMed Web of Science ®Google Scholar
• E. Balsells, et al. The relative invasive disease potential of Streptococcus pneumoniae among children after PCV introduction: A systematic review and meta-analysis, J. Infect. 77 (2018), pp. 368–378.
   PubMed Web of Science ®Google Scholar
• S.D. Brugger, L.J. Hataway, and K. Mühlemann, Detection of streptococcus pneumoniae strain cocolonization in the nasopharynx, J. Clin. Microbiol. 47 (2009), pp. 1750–1756.
   PubMed Web of Science ®Google Scholar
• C. Bottomley, A. Roca, P.C. Hill, B. Greenwood, and V. Isham, A mathematical model of serotype replacement in pneumococcal carriage following vacciation, J. R. Soc. Interfact. 10 (2013), pp. 20130786. http://dx.doi.org/10.1098/rsif.2013.0786.
   PubMed Web of Science ®Google Scholar
• Centers for Disease Control and Prevention. Vital Statistics Rapid Release: Births: Provisional Data for 2018. Available at https://www.cdc.gov/nchs/data/vsrr/vsrr-007-508.pdf (accessed Jan 3 2020).
   Google Scholar
• Centers for Disease Control and Prevention. National Center for Health Statistics: Mortality in the United States, preprint (2017). Available at https://www.cdc.gov/nchs/products/databriefs/db328.htm (accessed Jan 2 2020).
   Google Scholar
• Centers for Disease Control and Prevention. 2017. Active Bacterial Core Surveillance Report, Emerging Infections Program Network, Streptococcus pneumoniae, preprint (2017). Available at via the internet: http://www.cdc.gov/abcs/reportsfindings/survreports/spneu17.pdf (accessed May 14 2019).
   Google Scholar
• Centers for Disease Control and Prevention. ChildVaxView: 2002 through 2017 Childhood Pneumococcal Conjugate Vaccine (PCV) Coverage Trend Report, Available at https://www.cdc.gov/vaccines/imz-managers/coverage/childvaxview/data-reports/pcv/trend/index.html (accessed Jan 7 2020).
   Google Scholar
• S. Cobey and M. Lipsitch, Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes, Science 335 (2012), pp. 1376–1380.
   PubMed Web of Science ®Google Scholar
• Y.H. Choi, M. Jit, N. Gay, N. Andrews, P.A. Waight, A. Melegaro, R. Georege, and E. Miller, 7-Valent pneumococcal conjugate vaccination in England and Wales: Is it still beneficial despite high levels of serotype replacement?, PLoS One 6(10) (2011), pp. e26190. doi:10.1371/journal.pone.0026190.
   PubMed Web of Science ®Google Scholar
• Y.H. Choi, M. Jit, S. Flasche, N. Gay, and E. Miller, Mathematical modelling long-term effects of replacing Prevnar7 with Prevnar13 on invasive pneumococcal diseases in England and Wales, PLoS One 7(7) (2012), pp. e39927. doi:10.1371/journal.pone.0039927..
   PubMed Web of Science ®Google Scholar
• A.P. Desai, et al. Decline in pneumococcal nasopharyngeal carriage of vaccine serotypes after the introduction of the 13-valent pneumococcal conjugate vaccine in children in Atlanta Georgia, Pediatr. Infect. Dis. J. 34 (2015), pp. 1168–1174.
   PubMed Web of Science ®Google Scholar
• P. Driessche and J. Watmough, Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission, Math. Biosci. 180 (2002), pp. 29–48.
   PubMed Web of Science ®Google Scholar
• O. Diekmann, J.A.P. Heesterbeek, and J.A.J. Metz, On the definition and the computation of the basic reproduction ratio Ro in models for infectious diseases in heterogeneous populations, J. Math. Biol.28 (1990), pp. 365–382.
   PubMed Web of Science ®Google Scholar
• E. Delgleize, O. Leeuwenkamp, E. Theodorou, and N. Van de Velde, Cost effectiveness analysis of routine pneumococcal vaccination in the UK: A comparison of the PHiD-CV vaccine and the PCV-13 vaccine using a Markov model, BMJ Open 6 (2016), pp. e010776. doi:10.1136/bmjopen-2015-010776..
   PubMed Web of Science ®Google Scholar
• E.H. Elbasha and A. Galvani, Vaccination against multiple HPV types, Math. Biosci. 197 (2005), pp. 88–117.
   PubMed Web of Science ®Google Scholar
• S. Flasche, W.J. Edmunds, E. Miller, D. Goldblatt, C. Robertson, and Y.H. Choi, The impact of specific and non-specific immunity on the ecology of Streptococcus pneumoniae and the implications for vaccination, Proc. R. Soc. B 280 (2013), pp. 20131939. http://dx.doi.org/10.1098/rspb.2013.1939.
   PubMed Web of Science ®Google Scholar
• G. Falkenhorst, C. Remschmidt, T. Harder, O. Wichmann, S. Glodny, E. Hummers-Pradier, T. Ledig, and C. Bogdan, Background paper to the updated pneumococcal vaccination recommendation for older adults in Germany, Bundesgesundheitsblatt 59 (2016), pp. 1623–1657. DOI 10.1007/s00103-016-2466-9.
   Google Scholar
• S. Flasche, J. Ojal, O.L.P de Waroux, M. Otiende, K.L. O'Brien, M. Kiti, D.J. Nokes, W.J. Edmunds, and J.A.G. Scott, Assessing the efficiency of catch-up campaigns for the introduction of pneumococcal conjugate vaccine: A modelling study based on data from PCV10 introduction in Kilifi, Kenya, BMC Med. 15(1) (2017), pp. 113.
   PubMed Web of Science ®Google Scholar
• E. Gjini, Geographic variation in pneumococcal vaccine efficacy estimated from dynamic modeling of epidemiological data post-PCV7, Sci. Rep. 7 (2017), pp. 3049. DOI:10.1038/s41598-017-02955-y.
   PubMed Web of Science ®Google Scholar
• L.R. Grant, et al. Impact of the 13-valent pneumococcal conjugate vaccine on pneumococcal carriage among American indians, Pediatr. Infect. Dis. J. 35(8) (2016), pp. 907–914.
   PubMed Web of Science ®Google Scholar
• E. Gjini and M.G.M. Gomes, Expanding vaccine efficacy estimation with dynamic models fitted to cross-sectional prevalence data post-licensure', Epidemics 14 (2016), pp. 71–82.
   PubMed Web of Science ®Google Scholar
• S.M. Granat, J. Ollgren, E. Herva, Z. Mia, K. Auranen, and P.H. Mäkelä, Epidemiological evidence for serotype-independent acquired immunity to pneumococcal carriage, J. Infect. Dis. 200 (2009), pp. 99–106.
   PubMed Web of Science ®Google Scholar
• E. Gjini, C. Valente, R. Sá-Leão, and M.G.M. Gomes, How direct competition shapes coexistence and vaccine effects in multi-strain pathogen systems, J. Theor. Biol. 388 (2016), pp. 50–60.
   PubMed Web of Science ®Google Scholar
• M. Gaivão, F. Dionisio, and E. Gjini, Transmission fitness in co-colonization and the persistence of bacterial pathogens, Bull Math Biol 79 (2017), pp. 2068–2087.
   PubMed Web of Science ®Google Scholar
• H.W. Hethcote, The mathematics of infectious diseases, SIAM Rev. 42(4) (2000), pp. 599–653.
   Web of Science ®Google Scholar
• W.P. Hausdorff and W.P. Hanage, Interim results of an ecological experiment – conjugate vaccination against the pneumococcus and serotype replacement, Hum. Vaccin Immunother. 12 (2016), pp. 358–74.
   PubMed Web of Science ®Google Scholar
• M. Habib, B.D. Porter, and C. Satzke, Capsular serotyping of streptococcus pneumoniae using the quellung reaction, J. Vis. Exp. JoVE (2014). doi:10.3791/51208.
   PubMed Web of Science ®Google Scholar
• M. Iannelli, M. Martcheva, and X. Li, Strain replacement in an epidemic model with super-infection and perfect vaccination, Math. Biosci. 195 (2005), pp. 23–46.
   PubMed Web of Science ®Google Scholar
• M. Lipsitch, Vaccination against colonizing bacteria with multiple serotypes, Proc. Natl. Acad. Sci. USA 94 (1997), pp. 6571–6576.
   PubMed Web of Science ®Google Scholar
• M. Lipsitch, Bacterial vaccines and serotype replacement: Lessons from Haemophilus influenzae and prospects for Streptococcus pneumoniae, Emerg. Infect. Dis. 5(3) (1999), pp. 336–45.
   PubMed Web of Science ®Google Scholar
• M. Lipsitch, et al. Estimating rates of carriage acquisition and clearance and competitive ability for pneumococcal Serotypes in Kenya with a Markov transition model, Epidemiology 23(4) (2012), pp. 510.
   PubMed Web of Science ®Google Scholar
• A. Lochen and R.M. Anderson, Dynamic transmission models and economic evaluations of pneumococcal conjugate vaccines: A quality appraisal and limitations, Clin. Microbiol. Inf. (2019). https://doi.org/10.1016/j.cmi.2019.04.026.
   Google Scholar
• C.D.S. Lefebvre, A. Terlinden, and B. Standaert, Dissecting the indirect effects caused by vaccines into the basic elements, Hum. Vaccin. Immunother. 11(9) (2015), pp. 2142–2157. doi:10.1080/21645515.2015.1052196.
   PubMed Web of Science ®Google Scholar
• I.J. Myung, Tutorial on maximum likelihood estimation, J. Math. Psychol. 47 (2003), pp. 90–100.
   Web of Science ®Google Scholar
• A. Melegaro, Y. Choi, R. Pebody, and N. Gay, Pneumococcal carriage in United Kingdom families: Estimating serotype-specific transmission parameters from longitudinal data, Am. J. Epidemiol. 166 (2007), pp. 228–235.
   PubMed Web of Science ®Google Scholar
• A. Melegaro, Y.H. Choi, R. George, W.J. Edmunds, E. Miller, and N.J. Gay, Dynamic models of pneumococcal carriage and the impact of the heptavalent pneumococcal conjugate vaccine on invasive pneumococcal disease, BMC Infect. Dis. 10 (2010), pp. 90.
   PubMed Web of Science ®Google Scholar
• E. Miller, N.J. Andrews, P.A. Waight, M.P.E. Slack, and R.C. George, Herd immunity and serotype replacement 4 years after seven-valent pneumococcal conjugate vaccination in England and Wales: An observational cohort study, Lancet Infect. Dis. 11 (2011), pp. 760–68. doi:10.1016/S1473-3099(11)70090-1.
   PubMed Web of Science ®Google Scholar
• J. Mehtälä, M. Antonio, M.S. Kaltoft, K.L. O'Brien, and K. Auranen, Competition between streptococcus pneumoniae strains: Implications for vaccine-induced replacement in colonization and disease, Epidemiology 24(4) (2013), pp. 522–29.
   PubMed Web of Science ®Google Scholar
• G. Masala, M. Lipsitch, C. Bottomley, and S. Flasche, Exploring the role of competition induced by non-vaccine serotypes for herd protection following pneumococcal vaccination, J. R. Soc. Interface 14 (2017), pp. 20170620. http://dx.doi.org/10.1098/rsif.2017.0620.
   PubMed Web of Science ®Google Scholar
• A. Matanock, G. Lee, R. Gierke, M. Kobayashi, A. Leidner, and T. Pilishvili, Use of 13-valent pneumococcal conjugate vaccine and 23-valent pneumococcal polysaccharide vaccine among adults aged ≥65 years: Updated recommendations of the advisory committee on immunization practices, Morb. Mortal. Wkly. Rep. 68 (2019), pp. 1069–1075.
   PubMed Web of Science ®Google Scholar
• Merck Sharp & Dohme Corp. A Study to Evaluate the Safety, Tolerability, and Immunogenicity of V114 Followed by PNEUMOVAXTM23 in Healthy Adults 50 Years of Age or Older (V114-016/PNEU-PATH), preprint (2018). Available at https://clinicaltrials.gov/ct2/show/NCT03480763?term=NCT03480763&rank=1.
   Google Scholar
• Merck Sharp & Dohme Corp. A Study to Evaluate the Safety, Tolerability, and Immunogenicity of V114 Followed by PNEUMOVAXTM23 in Adults Infected With Human Immunodeficiency Virus (HIV) (V114-018/PNEU-WAY), preprint (2019). Available at https://clinicaltrials.gov/ct2/show/NCT03480802.
   Google Scholar
• Pfizer. Trial to Evaluate the Safety and Immunogenicity of a 20-valent Pneumococcal Conjugate Vaccine in Pneumococcal Vaccine-naive Adults, preprint (2019). Available at https://clinicaltrials.gov/ct2/show/NCT03760146?term=NCT03760146&rank=1.
   Google Scholar
• E. Numminen, L. Cheng, M. Gyllenberg, and J. Corander, Estimating the transmission dynamics of Streptococcus pneumoniae from strain prevalence data, Biometrics 69(3) (2013), pp. 748–57.
   PubMed Web of Science ®Google Scholar
• K. Okuneye and A.B. Gumel, Analysis of a temperature and rainfall-dependent model for malaria transmission dynamics, Math. Biosci. 287 (2017), pp. 72–92.
   PubMed Web of Science ®Google Scholar
• K. Prem, A.R. Cook, and M. Jit, Projecting social contact matrices in 152 countries using contact surveys and demographic data, PLoS Comput. Biol. 13(9) (2017), pp. e1005697. https://doi.org/10.1371/journal.pcbi.1005697.
   PubMed Web of Science ®Google Scholar
• H. Rinta-Kokko, R. Dagan, N. Givon-Lavi, and K. Auranen, Estimation of vaccine efficacy against acquisition of pneumococcal carriage, Vaccine 27 (2009), pp. 3831–3837.
   PubMed Web of Science ®Google Scholar
• H.L. Smith, Monotone dynamical systems: An introduction to the theory of competitive and cooperative systems, American Math. Soc., Providence, (1995).
   Google Scholar
• S.J. Snedecor, D.R. Strutton, V. Ciuryla, E.J. Schwartz, and M.F. Botteman, Transmission-dynamic model to capture the indirect effects of infant vaccination with prevnar (7-valent pneumococcal conjugate vaccine (pCV7) in older populations, Vaccine 27 (2009), pp. 4694–4703.
   PubMed Web of Science ®Google Scholar
• K.L. Sutton, H.T. Banks, and C. Castillo-Chavez, Public vaccination policy using an age-structured model of pneumococcal infection dynamics, J. Biol. Dyn. 4(2) (2010), pp. 176–195.
   PubMedGoogle Scholar
• B. Simell, K. Auranen, H. Käyhty, D. Goldblatt, R. Dagan, and K.L. O'Brien, The fundamental link between pneumococcal carriage and disease, Expert Rev. Vaccines 11(7) (2012), pp. 841–855.doi:10.1586/erv.12.53.
   PubMed Web of Science ®Google Scholar
• A.M.C. Sartori, L.M. Rozman, T.C. Decimoni, R. Leandro, H.M.D. Novaes, and P.C. de Soárez, A systematic review of health economic evaluations of vaccines in Brazil, Hum. Vaccines Immunother.13(6) (2017), pp. 1454–1465.
   PubMed Web of Science ®Google Scholar
• L. Temime, D. Guillemot, and P.Y. Boëlle, Short- and long-term effects of pneumococcal conjugate vaccination of children penicillin resistance, Antimicrob. Agents Chemother. 48(6) (2004), pp. 2206–2213.
   PubMed Web of Science ®Google Scholar
• L. Temime, P.Y. Boëlle, AlJ. Valleron, and D. Guillemot, Penicillin-resistant pneumococcal meningitis: High antibiotic exposure impedes new vaccine protection, Epidemiol. Infect. 133 (2005), pp. 493–501.
   PubMed Web of Science ®Google Scholar
• P. Turner, J. Hinds, C. Turner, A. Jankhot, K. Gould, S.D. Bentley, F. Nosten, and D. Goldblatt, Improved detection of nasopharyngeal cocolonization by multiple pneumococcal serotypes by use of latex agglutination or molecular serotyping by microarray, J. Clin. Microbiol. 49 (2011), pp. 1784–1789.
   PubMed Web of Science ®Google Scholar
• D. Thorrington, N. Andrews, J. Stowe, E. Miller, and A.J. van Hoek, Elucidating the impact of the pneumococcal conjugate vaccine programme on pneumonia, sepsis and otitis media hospital admissions in England using a composite control, BMC Med. 16 (2018), pp. 13.
   PubMed Web of Science ®Google Scholar
• T. van Effelterre, M.R. Moore, F. Fierens, C.G. Whitney, L. White, S.I. Pelton, and W.P. Hausdorff, A dynamic model of pneumococcal infection in the United States: Implications for prevention through vaccination, (2010).
   Google Scholar
• A.J. van Hoek, N.J. Andrews, P.A. Waight, R.C. George, and E. Miller, Effect of serotype on focus and mortality of invasive pneumococcal disease: Coverage of different vaccines and insight into non-vaccine serotypes, PLoS One 7(7) (2012), pp. e39150. doi:10.1371/journal.pone.0039150.
   PubMed Web of Science ®Google Scholar
• D. Weinberger, R. Malley, and M. Lipsitch, Serotype replacement in disease after pneumococcal vaccination, Lancet 378 (2011), pp. 1962–1973. DOI:10.1016/S0140-6736(10)62225-8.
   PubMed Web of Science ®Google Scholar
• D.B. Wu, C. Chang, Y. Huang, Y. Wen, C. Wu, and C.S. Fann, Cost-effectiveness analysis of pneumococcal conjugate vaccine in Taiwan: A transmission dynamic modeling approach, Value Health 15 (2012), pp. S15–S19.
   PubMed Web of Science ®Google Scholar
• A.L. Wyllie, M.L.J.N. Chu, M.H.B. Schellens, J.V.E. Gastelaars, M.D. Jansen, A. van der Ende, D.Bogaert, E.A.M. Sanders, and K. Trzciński, Streptococcus pneumoniae in saliva of dutch primary school children, PloS One 9(7) (2014), pp. e102045.
   PubMed Web of Science ®Google Scholar
• B. Wahl, K.L. O'Brien, A. Greenbaum, A. Majumder, L. Liu, and Y. Chu, et al. Burden of streptococcus pneumoniae and Haemophilus influenzae type b disease in children in the era of conjugate vaccines: Global, regional, and national estimates for 2000-15, Lancet Glob. Health 6 (2018), pp. e744–e757.
   PubMed Web of Science ®Google Scholar
• M. Wasserman, M.G. Palacios, A.G. Grajales, F.B. Baez-Revueltas, M. Wilson, C. McDade, and R.Farkouh, Modeling the sustained use of the 13-valent pneumococcal conjugate vaccine compared to switching to the 10-valent vaccine in Mexico, Hum. Vaccines Immunother. 15(3) (2018), pp. 560–569. doi:10.1080/21645515.2018.1516491.
   PubMed Web of Science ®Google Scholar