Meningococcal Genetic Variation Mechanisms Viewed through Comparative Analysis of Serogroup C Strain FAM18

Stephen D Bentley ,Sally Whitehead,Mark Achtman,Julian Parkhill,Carol Churcher,Louise Unwin,Bart Barrell,Mark Maddison,Sharon Moule,Tracey Chillingworth,Ann Cronin,Kay Jagels,Ester Rabbinowitsch,Sarah Sharp,Lori Snyder ,N Saunders ,George Vernikos ,C Arrowsmith ,Paul A Davis ,Michael A Quail ,Nancy Holroyd

doi:10.1371/journal.pgen.0030023

Abstract

The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements) provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an impact on the interaction with the host tissues, and understanding these mechanisms is important to aid our understanding of the intimate and complex relationship between the human nasopharynx and the meningococcus.

Highlights

N. meningitidis colonizes the nonciliated columnar mucosal cells of the human nasopharynx as a harmless commensal organism and, as such, is carried by five to ten percent of the adult population [1,2]
We report the genome sequence of N. meningitidis serogroup C strain FAM18, a medically important representative of the ET-37/ST-11 complex, which has been a major cause of meningococcal disease worldwide throughout the last century [19] and, despite low carriage rates, continues to be associated with sporadic outbreaks [20,21,22,23]
We have previously suggested that these neisserial intergenic mosaic element (NIME) arrays may encourage sequence variation in neighbouring genes by increasing the frequency of recombination with exogenous DNA, and exchange of adjacent sequences, either by acting as substrates for homologous recombination, or as targets for a specific recombinase [17]

Summary

Introduction

N. meningitidis (the meningococcus) colonizes the nonciliated columnar mucosal cells of the human nasopharynx as a harmless commensal organism and, as such, is carried by five to ten percent of the adult population [1,2]. Some strains are able to cross the mucosa into the bloodstream from where they can cause septicaemia or meningitis and, as a result, are a major cause of disease worldwide [2]. Several genetic loci have been associated with disease [3,4], but for most strains the mechanism of virulence is not well defined. The close interaction with the human host is reflected in enriched diversity and variability at the bacterial cell surface. Vaccines targeted to the capsule types most commonly associated with disease have been successful, though capsule switching is a cause of concern [8]. Many meningococcal surface-exposed proteins and carbohydrates are highly variable, creating a major challenge in the development of a universal meningococcal vaccine [9,10]

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