Estimates of the reproductive numbers and demographic reconstruction of outbreak associated with C:P1.5–1,10–8:F3–6:ST–11(cc11) Neisseria meningitidis strains

Anderson, 1991, 768 Andrews, 2010 Aubert, 2015, Serogroup C invasive meningococcal disease among men who have sex with men and in gay-oriented social venues in the Paris region: July 2013 to December 2014, Euro Surveill., 20, 21016, 10.2807/1560-7917.ES2015.20.3.21016 Bouckaert, 2014, BEAST 2: a software platform for Bayesian evolutionary analysis, PLoS Comput. Biol., 10, 10.1371/journal.pcbi.1003537 Caugant, 2009, Meningococcal carriage and disease - population biology and evolution, Vaccine, 27, B64, 10.1016/j.vaccine.2009.04.061 Chen, 2016, Basic reproduction number and transmission dynamics of common serogroups of enterohemorrhagic Escherichia coli, Appl. Environ. Microbiol., 30, 5612, 10.1128/AEM.00815-16 Croucher, 2011, Rapid pneumococcal evolution in response to clinical interventions, Science, 331, 430, 10.1126/science.1198545 Dress, 2008, Noisy: identification of problematic columns in multiple sequence alignments, Algorithms Mol Biol., 24, 7, 10.1186/1748-7188-3-7 Drummond, 2007, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evol. Biol., 7, 214, 10.1186/1471-2148-7-214 Drummond, 2002, Serially sampled data, Genetics, 161, 1307, 10.1093/genetics/161.3.1307 Drummond, 2005, Bayesian coalescent inference of past population dynamics from molecular sequences, Mol. Biol. Evol., 22, 1185, 10.1093/molbev/msi103 European Centre for Disease Prevention and Control (ECDC), 2013, Invasive meningococcal disease among men who have sex with men. Rapid risk assessment Fazio, 2009, Characterisation of Neisseria meningitidis C strains causing two clusters in the north of Italy in 2007 and 2008, Euro Surveill., 14, 19179, 10.2807/ese.14.16.19179-en Gay, 1995, Interpretation of serological surveillance data for measles using mathematical models: implications for vaccine strategy, Epidemiol. Infect., 115, 139, 10.1017/S0950268800058209 Harrison, 2013, Description and nomenclature of Neisseria meningitidis capsule locus, Emerg. Infect. Dis., 19, 566, 10.3201/eid1904.111799 Holmes, 1998, Molecular epidemiology and evolution of emerging infectious diseases, Br. Med. Bull., 54, 533, 10.1093/oxfordjournals.bmb.a011708 Italian National Health Institute (Istituto Superiore di Sanità, ISS) Jafri, 2013, Global epidemiology of invasive meningococcal disease, Popul. Health Metrics, 10, 17, 10.1186/1478-7954-11-17 Jolley, 2010, BIGSdb: scalable analysis of bacterial genome variation at the population level, BMC. Bioinformatics., 11, 595, 10.1186/1471-2105-11-595 Joshi, 2011 Koch, 2016, Evaluation of a temporary vaccination recommendation in response to an outbreak of invasive meningococcal serogroup C disease in men who have sex with men in Berlin, 2013-2014, Euro. Surveill., 21, 30122, 10.2807/1560-7917.ES.2016.21.5.30122 Kühnert, 2018, Tuberculosis outbreak investigation using phylodynamic analysis, Epidemics, 25, 47, 10.1016/j.epidem.2018.05.004 Lamelas, 2014, Emergence of a new epidemic Neisseria meningitidis serogroup A clone in the African meningitis belt: high resolution picture of genomic changes that mediate immune evasion, MBio, 21 Lo Presti, 2019, Reconstruction of dispersal patterns of Hypervirulent meningococcal strains of Serogroup C:cc11 by Phylogenomic time trees, J. Clin. Microbiol., 23 Maiden, 1998, Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms, Proc. Natl. Acad. Sci. U. S. A., 95, 3140, 10.1073/pnas.95.6.3140 Marcus, 2013, A cluster of invasive meningococcal disease in young men who have sex with men in Berlin, October 2012 to May 2013, Euro Surveill., 18, 20523, 10.2807/1560-7917.ES2013.18.28.20523 Marttinen, 2011, Detection of recombination events in bacterial genomes from large population segments, Nucleic Acids Res., 40 Menichetti, 2018, Invasive Meningococcal Disease due to group C N. meningitidis ST11 (cc11): the Tuscany cluster 2015-2016, Vaccine, 25, 5962, 10.1016/j.vaccine.2018.08.050 Méric, 2015, Ecological overlap and horizontal gene transfer in Staphylococcus aureus and Staphylococcus epidermidis, Genome. Biol. Evol., 16, 1313, 10.1093/gbe/evv066 Moore, 1991, Meningococcal meningitis in sub-Saharan Africa: a model for the epidemic process, Clin. Infect. Dis., 14, 515, 10.1093/clinids/14.2.515 Moura, 2017, Molecular characterization of Neisseria meningitidis isolates recovered from 11-19-year-old meningococcal carriers in Salvador, Brazil, PLoS One, 20 Pekka, 2008, Bayesian modeling of recombination events in bacterial populations, BMC. Bioinformatics, 9, 421, 10.1186/1471-2105-9-421 Pérez-Losada, 2018, Microbial sequence typing in the genomic era, Infect. Genet. Evol., 63, 346, 10.1016/j.meegid.2017.09.022 Pezzotti, 2018, Meningococcal C conjugate vaccine effectiveness before and during an outbreak of invasive meningococcal disease due to Neisseria meningitidis serogroup C/cc11, Tuscany, Italy, Vaccine., 5, 4222, 10.1016/j.vaccine.2018.06.002 Posada, 2008, jModelTest: phylogenetic model averaging, Mol. Biol. Evol., 25, 1253, 10.1093/molbev/msn083 R Development Core Team, 2008 Rosenstein, 2001, Commentary: opportunities to decrease mortality and long-term sequellae associated with meningococcal disease in Africa, Int. J. Epidemiol., 30, 1447, 10.1093/ije/30.6.1447 Rouphael, 2012, Neisseria meningitidis: biology, microbiology, and epidemiology, Methods Mol. Biol., 799, 1, 10.1007/978-1-61779-346-2_1 Schuchat, 1997, Bacterial meningitis in the United States in 1995. Active Surveillance Team, N. Engl. J. Med., 337, 970, 10.1056/NEJM199710023371404 Simpson, 2009, ABySS: a parallel assembler for short read sequence data, Genome Res., 19, 1117, 10.1101/gr.089532.108 Stadler, 2012, Estimating the basic reproductive number from viral sequence data, Mol. Biol. Evol., 29, 347, 10.1093/molbev/msr217 Stadler, 2013, Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV), Proc. Natl. Acad. Sci. U. S. A., 2, 228, 10.1073/pnas.1207965110 Stefanelli, 2016, Genome-based study of a spatio-temporal cluster of invasive meningococcal disease due to Neisseria meningitidis serogroup C, clonal complex 11, J. Inf. Secur., 73, 136 Stefanelli, 2016, Increased incidence of invasive meningococcal disease of serogroup C / clonal complex 11, Tuscany, Italy, 2015 to 2016, Euro Surveill., 21, 30176, 10.2807/1560-7917.ES.2016.21.12.30176 Stephens, 1999, Uncloaking the meningococcus: dynamics of carriage and disease, Lancet, 353, 941, 10.1016/S0140-6736(98)00279-7 Stephens, 2007, Epidemic meningitis, meningococcaemia, and Neisseria meningitidis, Lancet, 369, 2196, 10.1016/S0140-6736(07)61016-2 Tamura, 2013, MEGA6: molecular evolutionary genetics analysis version 6.0, Mol. Biol. Evol., 30, 2725, 10.1093/molbev/mst197 Trotter, 2005, Dynamic models of meningococcal carriage, disease, and the impact of serogroup C conjugate vaccination, Am. J. Epidemiol., 1, 89, 10.1093/aje/kwi160 Weiss, 2013, Control of recent community-based outbreaks of invasive meningococcal disease in men who have sex with men in Europe and the United States, Euro Surveill., 18, 20522, 10.2807/1560-7917.ES2013.18.28.20522 Yazdankhah, 2004, Distribution of serogroups and genotypes among disease-associated and carried isolates of Neisseria meningitidis from the Czech Republic, Greece, and Norway, J. Clin. Microbiol., 42, 5146, 10.1128/JCM.42.11.5146-5153.2004