Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks

Abstract

BackgroundWhile overall rates of meningococcal disease have been declining in the United States for the past several decades, New York City (NYC) has experienced two serogroup C meningococcal disease outbreaks in 2005–2006 and in 2010–2013. The outbreaks were centered within drug use and sexual networks, were difficult to control, and required vaccine campaigns.MethodsWhole Genome Sequencing (WGS) was used to analyze preserved meningococcal isolates collected before and during the two outbreaks. We integrated and analyzed epidemiologic, geographic, and genomic data to better understand transmission networks among patients. Betweenness centrality was used as a metric to understand the most important geographic nodes in the transmission networks. Comparative genomics was used to identify genes associated with the outbreaks.ResultsNeisseria meningitidis serogroup C (ST11/ET-37) was responsible for both outbreaks with each outbreak having distinct phylogenetic clusters. WGS did identify some misclassifications of isolates that were more distant from the outbreak strains, as well as those that should have been included based on high genomic similarity. Genomes for the second outbreak were more similar than the first and no polymorphism was found to either be unique or specific to either outbreak lineage. Betweenness centrality as applied to transmission networks based on phylogenetic analysis demonstrated that the outbreaks were transmitted within focal communities in NYC with few transmission events to other locations.ConclusionsNeisseria meningitidis is an ever changing pathogen and comparative genomic analyses can help elucidate how it spreads geographically to facilitate targeted interventions to interrupt transmission.

Reactive vaccination as control strategy for an outbreak of invasive meningococcal disease caused by Neisseria meningitidis C:P1.5-1,10-8:F3-6:ST-11(cc11), Bergamo province, Italy, December 2019 to January 2020

“…We identified an outbreak caused by a highly transmissible and hypervirulent MenC/cc11 strain. The same strain was has caused several outbreaks worldwide [ 2 , 3 , 5 - 8 ].…”

“…Cases of IMD caused by MenC/cc11 are often associated with sepsis and with a high case fatality rate (CFR) and sequelae [ 4 ]. Several outbreaks and epidemics due to MenC/cc11 have been described worldwide since the mid-1980s [ 3 , 5 ]; since 2013, outbreaks have been reported also in European countries such as Belgium, France, Germany, Italy and the United Kingdom (UK) [ 6 - 9 ].…”

Evolution of Sequence Type 4821 Clonal Complex Hyperinvasive and Quinolone-Resistant Meningococci

“…Shanghai CDC sequenced 76 CC4821 isolates with Illumina HiSeq (Illumina, https://www.illumina.com ) using paired-end 150 base reads as previously described ( 13 ). An additional 97 publicly available CC4821 genomes consisted of 48 genomes from 14 provinces of China, including the reference strain 053442 ( 6 – 8 ) and 49 genomes from countries outside of China, including the United Kingdom (n = 20), United States (n = 8), and 11 other countries (n = 21) ( Figure 1 ; Appendix 1 Table 1) ( 10 , 12 , 14 – 17 ). The completeness and contamination of the genomes were evaluated using CheckM ( 18 ).…”

Relaciones de estructura-función en la P-glicoproteína humana (ABCB1): Perspectivas de las simulaciones de dinámica molecular

“…En 2002-2003, el coronavirus del síndrome respiratorio agudo severo (SARS-CoV) fue la primera enfermedad infecciosa para la cual, los científicos compartieron software y datos genéticos de patógenos a través de Internet para responder rápidamente a la enfermedad. A partir de entonces, la epidemiología genómica se consolidó con las respuestas a H5N1, H1N1-2009 y otras cepas de influenza como H7N9 [2] y se ha expandido para responder a las enfermedades transmitidas por los alimentos y de transmisión sexual [3][4][5]. El primer genoma del SARS-CoV se compartió después de la publicación [6,7] en el sitio web GenBank del Centro Nacional de Información Biotecnológica (NCBI), lo cual era lo habitual.…”