Meningococcal carriage in Dutch adolescents and young adults; a cross-sectional and longitudinal cohort study M.B. van Ravenhorst, M.W. Bijlsma, M.A.

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Meningococcal carriage in Dutch adolescents and young adults; a cross-sectional and longitudinal cohort study M.B. van Ravenhorst, M.W. Bijlsma, M.A. van Houten, V.M.D. Struben, A.S. Anderson, J. Eiden, L. Hao, K.U. Jansen, H. Jones, N. Kitchin, L. Pedneault, E.A.M. Sanders, A. van der Ende Clinical Microbiology and Infection Volume 23, Issue 8, Pages 573.e1-573.e7 (August 2017) DOI: 10.1016/j.cmi.2017.02.008 Copyright © 2017 The Authors Terms and Conditions

Fig. 1 Flow-chart for inclusion and follow-up. Carriers were identified by culture of oropharyngeal swabs. Note. Oropharyngeal swabs and questionnaires of participants in the longitudinal study cohort were collected at enrolment and 3 months and 8 months after enrolment. Clinical Microbiology and Infection 2017 23, 573.e1-573.e7DOI: (10.1016/j.cmi.2017.02.008) Copyright © 2017 The Authors Terms and Conditions

Fig. 2 Meningococcal carriage prevalence by age cohort at the first visit identified by culture of oropharyngeal swabs. (a) Overall meningococcal carriage identified by culture of oropharyngeal swabs from all 1715 participants at the first visit. (b) Meningococcal serogroup B carriage prevalence at the first visit identified by each detection method for a subset of participants of whom a second swab was collected; Ouchterlony, rt-PCR and WGS of cultured isolates and direct rt-PCR of the second swab. Note. Error bars indicate 95% CI. Clinical Microbiology and Infection 2017 23, 573.e1-573.e7DOI: (10.1016/j.cmi.2017.02.008) Copyright © 2017 The Authors Terms and Conditions

Fig. 3 Phylogeny of carriage isolates based on comparative genomic analysis. (a) Meningococcal serogroup B carriage (n = 105). (b) Distribution of single nucleotide polymorphisms (SNPs) in MenB isolates from three participants showing persistence of carriage across three longitudinal visits. The visits (ring 1) and clonal complexes (CCs) (ring 2) were annotated in colour strips along the circular tree. In ring 2, CCs were labelled accordingly, whereas white strip represents non-typeable (NT). Tree branches were coloured to match CCs (inferred from the majority isolates of the cluster). The isolate IDs of three persistent cases (carriage isolates collected from three longitudinal visits) were highlighted in different colours. Persistent carriage in three different participants is accompanied by a progressive accumulation of SNPs and/or recombination events. The WGS of isolates from visit 1 for each individual was used as a baseline or reference data set. Vertical light grey lines for each of the visit 1 WGS data sets represent sequences that are not part of the N. meningitidis core genome and are shared in WGS of carriage isolates from visits 2/3. In each case, WGS of isolates collected at visits 2 and 3 revealed an accumulation of SNPs and/or recombination events. Clinical Microbiology and Infection 2017 23, 573.e1-573.e7DOI: (10.1016/j.cmi.2017.02.008) Copyright © 2017 The Authors Terms and Conditions

Figure S1. Comparisons of laboratory methods to identify meningococcal serogroup B as detected by real-time PCR and whoe genome sequencing of cultured isolates and direct PCR of the second swab at the first visit. Clinical Microbiology and Infection 2017 23, 573.e1-573.e7DOI: (10.1016/j.cmi.2017.02.008) Copyright © 2017 The Authors Terms and Conditions

Figure S2. Overall carrier state of longitudinal cohort over time identified by culture of oropharyngeal swab. Clinical Microbiology and Infection 2017 23, 573.e1-573.e7DOI: (10.1016/j.cmi.2017.02.008) Copyright © 2017 The Authors Terms and Conditions

Figure S3. Phylogeny of carriage isolates (n = 415) based on comparative genomic analysis. Clinical Microbiology and Infection 2017 23, 573.e1-573.e7DOI: (10.1016/j.cmi.2017.02.008) Copyright © 2017 The Authors Terms and Conditions