Content uploaded by Dominique A Caugant
Author content
All content in this area was uploaded by Dominique A Caugant on Jun 11, 2020
Content may be subject to copyright.
Neisseria meningitidis (the meningococcus) is a Gram-
negative, extracellular bacterium that asymptomat-
ically colonizes the mucosal surface of the oropharynx
of ~10% of the human population1 and is transmitted
between individuals through inhalation of respira-
tory secretions and saliva during close contact with a
carrier (FIG.1). Invasive meningococcal disease (IMD)
is a relatively rare event that occurs when the bacte-
rium traverses the mucosal epithelium and invades the
bloodstream. As observed for Haemophilus influenzae
and Streptococcus pneumoniae, the meningococcus may
cross the blood–brain barrier and disseminate to the
meninges. Systemic infection usually results in poten-
tially life-threatening meningitis and/or septicaemia,
but other forms of disease, such as pneumonia, arthri-
tis, urethritis and conjunctivitis, may also develop2.
In spite of more than five decades of effort to develop
effective meningococcal vaccines3,4 (BOX1), IMD contin-
ues to be a major global public health challenge, with
an estimated burden of disease of approximately one
million cases annually worldwide5 and overall mortality
ranging from 4% to 20%, depending on the infecting
strain and the age of the individual6. The incidence of
meningococcal disease is generally highest in infants
younger than 1 year, with half of the cases occurring in
children younger than 5 years. Another peak of IMD
can be seen in adolescents and young adults — the age
groups with the highest prevalence of oropharyngeal
carriage1,5. The course of the disease can be fulminant;
early recognition of symptoms is crucial, and imme-
diate treatment, including the administration of anti-
biotic therapy, is the only effective measure when IMD
has developed7. In addition, a substantial proportion of
survivors experience severe sequelae, such as deafness,
mental impairment and amputations8.
N. meningitidis is naturally competent for genetic
transformation and readily undergoes homologous
recombination9. Consequently, the genomic diversity
of meningococcal lineages is extensive, and recombina-
tion, rather than mutation10, is the predominant source
of new genetic information and the essential driving
force behind the evolution of the bacterium, permitting
rapid adaptation to fluctuating environmental condi-
tions. With whole-genome sequencing (WGS) becoming
relatively inexpensive, several thousand meningococcal
genomes, which are each ~2.2 million nucleotides in
length, are currently available for in-depth analyses.
This source of data, although still underutilized, is
starting to provide new insights into the plasticity of
the genome of this human commensal with occasional
pathogenic potential. In this Review, we discuss how
high-throughput sequencing approaches have advanced
Meninges
The membranes surrounding
the brain and spinal cord.
Fulminant
Coming on suddenly and with
great severity.
Neisseria meningitidis: using
genomics to understand diversity,
evolution and pathogenesis
DominiqueA.Caugant
1,2* and OlaB.Brynildsrud
1,3
Abstract | Meningococcal disease remains an important cause of morbidity and death worldwide
despite the development and increasing implementation of effective vaccines. Elimination of
the disease is hampered by the enormous diversity and antigenic variability of the causative agent,
Neisseria meningitidis, one of the most variable bacteria in nature. These features are attained
mainly through high rates of horizontal gene transfer and alteration of protein expression
through phase variation. The recent availability of whole-genome sequencing (WGS) of
large-scale collections of N. meningitidis isolates from various origins, databases to facilitate
storage and sharing of WGS data and the concomitant development of effective bioinformatics
tools have led to a much more thorough understanding of the diversity of the species, its
evolution and population structure and how virulent traits may emerge. Implementation of
WGS is already contributing to enhanced epidemiological surveillance and is essential to ascertain
the impact of vaccination strategies. This Review summarizes the recent advances provided
by WGS studies in our understanding of the biology of N. meningitidis and the epidemiology
of meningococcal disease.
1Division for Infection Control
and Environmental Health,
Norwegian Institute of Public
Health, Oslo, Norway.
2Department of Community
Medicine, Faculty of
Medicine, University of Oslo,
Oslo, Norway.
3Department of Food Safety
and Infection Biology, Faculty
of Veterinary Science,
Norwegian University of Life
Science, Oslo, Norway.
*e-mail: dominique.caugant@
fhi.no
https://doi.org/10.1038/
s41579-019-0282-6
REVIEWS
Nature reviews
|
Microbiology
our understanding of the diversity and evolution of
N. meningitidis and the pathogenesis of N. meningitidis
infection and are contributing to explaining the
epidemiology of meningococcal disease.
The genus Neisseria
The genus Neisseria comprises at least 25 species, most
of them colonizing the mucosal and dental surfaces of
warm-blooded animals, usually as harmless commen-
sals11,12. Of the 11 species colonizing humans, most are
non-pathogenic, although some may cause disease in
immunocompromised hosts. However, the two geneti-
cally closely related species N. meningitidis and Neisseria
gonorrhoeae (the gonococcus) are globally important
pathogens. The commensal species, as well as the gono-
coccus, are a reservoir of genes that can be acquired
by the meningococcus through horizontal genetic
transfer. DNA fragments several kilobases long can be
imported into N. meningitidis from related organisms
co-colonizing the mucosa13. A recent study using WGS
identified a core genome of 1,111 gene families conserved
among Neisseria species14. In particular, there is a high
level of sequence similarity (~96%) between the genomes
of the two human-specific pathogens N. meningitidis
and N. gonorrhoeae. Phylogenetic analy ses based on
sequencing of the 53 ribosomal genes have shown that
N. meningitidis and N. gonorrhoeae evolved recently
from a common ancestor15,16, but separated as a result of
colonization of distinct ecological niches (FIG.2). Whereas
N. gonorrhoeae has been documented in dental calculus
of Neanderthals17, the origin of meningo coccal disease
is probably only a few centuries old18. Genomic analy-
ses showed that an ancestral gonococcal strain acquired
a number of genetic factors allowing it to colonize the
oral mucosal surface instead of the urogenital environ-
ment19. One of the main differences between N. menin-
gitidis and N. gonorrhoeae is the lack of a capsule in the
gonococcus, whereas disease-causing meningo cocci in
immunocompetent individuals are nearlyalways encap-
sulated. On the basis of sequence similarity, it has been
hypothesized that the genes for capsule synthesis and
other virulence factors in meningococci were probably
acquired through horizontal gene transfer from mem-
bers of the family Pasteurellaceae after the phylogenetic
split20. Newer analyses that identified various genes of
the capsule operon in non-pathogenic Neisseria species
suggested multiple acquisition and loss events during the
evolution of the genus Neisseria21.
Epidemiology
Of the three main bacterial pathogens associated
with meningitis (H. influenzae, S. pneumoniae and
N. meningitidis), N. meningitidis is the only one (with
the exception of serotype 1 S. pneumoniae) that can
cause large outbreaks. Although meningococcal disease
frequently occurs endemically, with scattered and appar-
ently unrelated cases, large, devastating and unpredictable
epidemics may develop in some parts of the world, some-
times encompassing several continents (that is, a pan-
demic situation). A zone south of the Sahara, called the
‘African meningitis belt’22, which stretches from Senegal
in the West to Ethiopia in the East (encompassing parts
or the whole of 26 countries), has the highest incidence
of meningococcal disease in the world23. Historically,
incidence rates in that region have exceeded 800 cases
per 100,000 population per year during serogroup A
meningitis epidemics24.
b Oropharynx
a Transmission
Capsule
FetA, fHbp, NadA,
Opa and other
virulence factors
N. meningitidis
Carriage
Invasion
Peptidoglycan
Porin
Pilus
LOS
c Cell suface
Fig. 1 | Overview of Neisseria meningitidis transmission, carriage state, invasion and
virulence factors of the meningococcal outer membrane. a | Transmission occurs
through contact with respiratory droplets or secretions that enter through the mouth
or nose, with subsequent colonization and proliferation of bacteria in the oropharynx or
nasopharynx. b | In the proliferation phase, a wide range of phenotypic variation is
stochastically created by genetic reassortment through various mechanisms, especially
phase variation as a result of the expansion or contraction of repeat elements122, but also
intragenomic and intergenomic recombination and post-translational modification of
surface proteins146. Most N. meningitidis infections never result in clinical disease, and the
bacteria remain in a carriage state (illustrated in blue). However, for genetically primed
strains, a potentially invasive phenotype may eventually emerge in the proliferation
and reassortment phase (illustrated in red). Invasive phenotypes penetrate the mucosal
epithelium and gain access to the bloodstream. c | An invasive phenotype displays a
number of immunogenic molecules on its cell surface. They can be categorized broadly
into adhesins, invasins and iron acquisition systems. The outer membrane contains
type IV pili and the surface-bound proteins NadA and Opa, all of which function to allow
attachment to host cell surfaces and invasion through the mucosa. The membrane also
contains immune modulators such as factor H-binding protein (fHbp) and NspA (which
also binds complement factor H) and, in nearly all hypervirulent strains encountered to
date, the bacterium is surrounded by a polysaccharide capsule that protects against
complement-mediated phagocytosis. Additionally , the outer membrane of the bacterium
contains lipooligosaccharides (LOS; endotoxin), which have both adhesion and immune
evasion properties. Proteins such as ferric enterobactin transport protein (FetA) and
HmbR enable meningococci to acquire from the human host iron, a crucial growth factor
during disease. Meningococcal porins, class 1 porin (PorA) and PorB, are sometimes also
classified as virulence factors since they interact with the immune system of the host147.
Some fragments of inflammation-promoting peptidoglycan from the cell wall may also
be released during growth148. Parts a and b adapted with permission from REF.122, Elsevier.
Core genome
The set of genes that are present
in all (or nearly all) strains of a
species or population.
www.nature.com/nrmicro
Reviews
Twelve serogroups are defined on the basis of the
structure of the capsular polysaccharide, and six of
them (serogroups A, B, C, W, X and Y) are responsi-
ble for nearly all cases of disease worldwide6. Genomic
analysis of the capsule locus has been used to support
the serogroup nomenclature25. The incidence of disease
caused by the different serogroups is changing con-
stantly, both temporally and geographically, possibly as
a result of changes in the human population immune
status26. Large epidemics have traditionally been caused
by serogroup A meningococci. However, in high-income
countries these epidemics stopped in the 1970s, whereas
they continued in sub-Saharan Africa until the success-
ful introduction of a monovalent conjugate vaccine
against serogroup A disease in large-scale mass vacci-
nation campaigns, starting in 2010 (REF.27). In much of
the developed world, including North America, South
America, western Europe, Australia and New Zealand,
serogroup B was the cause of endemic and hyper endemic
disease in the last part of the twentieth century, with
serogroup C causing sporadic outbreaks and epidem-
ics7. Following the introduction of effective conjugate
vaccines in national vaccination programmes, the inci-
dence of serogroup C disease has decreased in the past
decade in many high-income countries28. In recent years,
there have been increases in the number of cases of IMD
caused by serogroup Y (first in the USA and then in
western Europe)29,30, as well as by serogroup W, mainly
in Africa, South America and Europe31–34.
Epidemiological studies using the large genetic varia-
bility of the meningococcus to identify specific lineages
or clonal complexes within the species have demon-
strated substantial differences in the invasive poten-
tial of strains. The first studies of genetic diversity and
population structure of N. meningitidis used variation
in a small number of housekeeping genes, first eluci-
dated through multilocus enzyme electrophoresis35,36 and
subsequently through multilocus sequence typing37. The
molecular epidemiological studies revealed the existence
of particularly virulent lineages: sequence types (STs)
highly associated with outbreaks and epidemics and
only rarely identified in samples from healthy carriers38.
With the increased availability and affordability of WGS,
a new era has been opened to tackle many issues regard-
ing the epidemiology of IMD, linked to the evolution
of this pathogen39,40. Clonal complexes first defined on
the basis of multilocus enzyme electrophoresis and con-
firmed by multilocus sequence typing are now scruti-
nized using WGS41,42. The Neisseria PubMLST database
currently includes more than 20,000 WGS-complete
genomes (genome size greater than 2 Mb) of Neisseria
species isolates, including more than 15,000 genomes
of N. meningitidis (accessed 14 June 2019). In spite of
the extensive recombination potential of the species,
there is strong congruence of the various classification
schemes. A phylogeny of a randomly sampled subset of
the meningococcal isolates in the database (~5% of all
isolates in the database) and their associated lineages is
shown in FIG.3.
Among the hypervirulent lineages identified in
N. meningitidis, lineage 11 is one of the most ancient,
identified in 1917. An interesting feature of lineage 11 is
its association with the four capsular serogroups contain-
ing polysialic acid (that is, serogroups B, C, W and Y).
Most of the lineage 11 isolates from the 1960s and 1970s
expressed the serogroup B capsule40, whereas in the 1990s
a new variant of ST-11 (designated as ST-11/ET-15)
gave rise to serogroup C outbreaks in North America
before spreading to Europe43. As a consequence, mono-
valent serogroup C conjugate vaccines were developed44.
Although serogroup W lineage 11 isolates already
existed in the 1970s, a severe epidemiological situation
occurred in 2000 when such isolates were introduced
in Saudi Arabia during the hajj pilgrimage, causing a
large outbreak. Following the hajj in 2000, the strain
spread worldwide, and ever since serogroup W line-
age 11 has been a problem, first in sub-Saharan Africa,
then in South America, Europe and Australia31–34,45–47.
WGS has been essential in elucidating the existence of
different clades of serogroup W lineage 11, providing
an understanding of their epidemiological importance.
With use of a gene-by-gene approach encompassing
1,546 core loci of 750 lineage 11 isolates, two sublin-
eages were differentiated; lineage 11.1 included the
strain introducedduring the hajj pilgrimage, whereas
lineage 11.2 included the South American strain and the
so-called original UK strain that emerged in the UK in
2009 (REF.40). Another new variant was identified in the
UK in 2013 that was associated with a severe increase
in serogroup W disease and has since spread to other
European countries34,48–50. Three putative recombina-
tional events and four point mutations distinguished
the UK 2013 strain from the original UK strain, includ-
ing genes encoding antigens, such as the haemoglobin–
haptoglobin receptor complex HpuAB, the genetic regu-
lator MtrR and a number of metabolic genes50. This
novel and rapidly expanding UK 2013 strain, which also
possesses the Neisseria adhesion A (NadA) antigen, has
been associated with unusualclinical features, including
Dental calculus
A form of hardened dental
plaque that is caused by
precipitation of minerals from
saliva and gingival fluid on the
teeth.
Multilocus enzyme
electrophoresis
A method for characterizing
organisms by the relative
mobilities under
electrophoresis of a large
number of intracellular
enzymes.
Multilocus sequence typing
A procedure to characterize
microbial isolates using the
DNA sequences of internal
fragments of multiple
housekeeping genes.
Box 1 | Genomics and meningococcal vaccines
There are effective protein-conjugate polysaccharide vaccines for four of the six
current disease-causing serogroups of Neisseria meningitidis126,127, and a low-cost
conjugate vaccine also including serogroup X is in a clinical phase II trial128. Such
conjugate vaccines are effective in infants, elicit longer-lasting immune responses and
may induce herd protection by affecting transmission of the bacterium in the human
population. Polysaccharide-based vaccines against serogroup B have not been pursued
owing to poor immunogenicity of the serogroup B capsule and self-antigen concerns129.
In the search for potential subcapsular antigens for a vaccine against serogroup B
disease, genomics has been essential. With use of the first available N. meningitidis
complete whole genome and an approach called ‘reverse vaccinology’130, novel protein
vaccine candidates were identified and recombinant DNA technology was used to
produce and test these antigens for suitability. The new targets, including a neisserial
adhesin NadA, the neisserial heparin-binding protein and factor H-binding protein
(fHbp) were combined with the outer membrane vesicle from a New Zealand vaccine
strain126 to produce Bexsero131. Given the known sequence diversity of fHbp132, another
protein-based vaccine, Trumenba, was developed to cover the two subfamilies of fHpb
and thus potentially target all of N. meningitidis serogroup B, and other serogroups as
well133. Large sequencing projects were undertaken to estimate the coverage of these
vaccines based on the diversity of the antigens among meningococcal populations
circulating in various geographical areas134,135. With whole-genome sequencing, any
set of antigen-encoding genes within a large collection of isolates can be efficiently
characterized and thus the potential coverage of different vaccines can be compared.
Whole-genome sequencing is also valuable in determining the changing prevalence of
the vaccine antigens following vaccine introduction and identifying escape mutants.
Nature reviews
|
Microbiology
Reviews
severe gastrointestinal symptoms51. Another variant
of lineage 11 has become adapted to colonization of
the urogenital tract, being transmitted mainly within the
population of men who have sex with men52–54 (BOX2).
Lineage 10 (previously designated as the ST-5 clonal
complex/lineage III)41, one of the three predominant
serogroup A lineages, has been responsible for major
epidemics of meningitis worldwide, but principally in
the meningitis belt of sub-Saharan Africa after its intro-
duction in the continent in 1988–1989 (REFS55,56). Three
successive waves of epidemics have occurred in the
meningitis belt associated with three distinct clones of
lineage 10, namely ST-5, ST-7 and ST-2859. As for lineage 11,
the principal antigens that invoke effective immunity
(for example, the class 1 porin (PorA), the ferric entero-
bactin transport protein (FetA) and factor H-binding
protein (fHbp))57,58 have remained unchanged in these
successive clones. Genome comparisons of the emerging
ST-2859 strains versus the ancestral ST-7 strains identi-
fied 13 recombination blocks, allowing replacement of
ST-7 by ST-2859 as a main cause of disease shortly after
ST-7 outbreaks. In 20% of the recombination events the
acquired DNA came from other species. The pgl locus,
which determines the glycosylation patterns of major
protein antigens, genes involved in the regulation of
pilus expression and genes involved in the synthesis
of maf3 adhesins were affected by the recombination
events58. Emergence and expansion of the ST-2859 clone
was explained by these changes in cell surface structures,
enabling the new clone to multiply in human popu-
lations having developed mucosal immunity against
ST-7. WGS analysis of 153 lineage 10 isolates covering
the successive epidemic waves provided conflicting
results. Although the genomes were highly uniform
within epidemic waves, with an average of 67.2% of all
loci exhibiting identical alleles, the emergence of the suc-
cessive epidemic clones was linked to 11 genetic events,
primarily involving core genes encoding metabolic pro-
cesses59. The acquired DNA was found to be identical to
that in unrelated, hyperinvasive meningococci, suggest-
ing that the epidemic clones emerged through the acqui-
sition of pre-existing metabolic gene variants rather
0.1
N. bergeri
N. polysaccharea
N. elongata
N. cinerea
N. lactamica
N. bacilliformis
N. shayeganii
N. canis
N. wadsworthi
N. weaveri
N. animaloris
N. zoodegmatis
N. musculi N. dentiae
N. iguanae N. animalis
N. subflava
N. mucosa and
N. sicca
N. oralis
N. gonorrhoeae
N. meningitidis
Human pathogens
Human commensals
Animal species
Fig. 2 | Phylogenetic network of the relationships between species in the genus Neisseria. Most species are distantly
related to each other and exhibit a variable degree of clonality. Intraspecies variation is large in Neisseria lactamica,
Neisseria oralis, Neisseria subflava, Neisseria cinerea, Neisseria polysaccharea and Neisseria elongata, with the latter
having multiple defined subspecies (Neisseria elongata subsp. elongata, Neisseria elongata subsp. glycolytica and
Neisseria elongata subsp. nitroreducens). At the other end of the spectrum, Neisseria gonorrhoeae is a particularly clonal
species, with all isolates clustering tightly together. The major pathogens, Neisseria meningitidis and N. gonorrhoeae,
are more closely related than other species within the genus. Species with overlapping ecology are more closely related
than those that inhabit distinct niches. For example, N. oralis, Neisseria mucosa, Neisseria sicca and N. subflava are all
non-pathogenic species that inhabit the human pharynx and are situated on the same branch. N. lactamica, N. cinerea,
N. polysaccharea and Neisseria bergeri are also non-pathogenic inhabitants of the human nasopharynx, although they
are each located on distinct branches of the phylogenetic tree. To date, there are no publicly available sequences for
Neisseria flava, and it is therefore not displayed in the figure. Note that N. sicca and N. mucosa did not form monophyletic
groups and were not distinguishable with this method, and could therefore possibly represent a single species or,
alternatively , more than two separate species. On the other hand, N. elongata, which is also found in the human pharynx,
is distantly related to other commensal species. The left side of the network is occupied by different distinct animal
strains. The figure was created as follows: 93 isolates were manually selected from the 21,615 isolates openly available
on the Neisseria PubMLST platform as of May 2019. For rare species, a minimum of two isolates were manually
selected. For N. meningitidis, one representative was selected from each defined clonal complex. For N. gonorrhoeae and
N. lactamica, representatives from the major sequence types were selected. In all cases, the selection procedure gave
preference to isolates that maximized geospatial and temporal variation. The network was created by concatenating
the sequences of all 53 loci included in the Neisseria ribosomal multilocus sequence typing scheme149, as defined in
PubMLST. The concatenated sequences were aligned with MAFFT150, and the Hamming distances from the resultant
distance matrix were fed to the Neighbor-Net algorithm151 as implemented in SplitsTree4 (REF.152). The scale bar
corresponds to a relative distance of 10% across the length of the alignment.
www.nature.com/nrmicro
Reviews
cc53
cc103, cc167
and cc865
cc282 and cc1157
cc32 (lineage 5)
cc35
cc269
cc41/44
c92, c175, cc335, cc364 and cc1572
cc5 (lineage 10)
cc60/162
cc461
cc23
cc22
cc213
cc18
cc198
cc181
cc8
cc10217
cc178
cc106
cc4821
cc11 (lineage 11)
1.0
100.0
0.1
a
bc
MLST cgMLST
Serogroup
C
W
NG
B
Fig. 3 | Phylogenetic networks of Neisseria meningitidis at different resolutions. a | Relationships between the
major clonal complexes (cc) defined in N. meningitidis using multilocus sequence typing (MLST). This network shows a
proportional representation of all N. meningitidis genomes submitted to PubMLST as of May 2019. The largest clonal
complexes are circled. Alternative lineage terminology is used for cc11 (lineage 11), cc5 (lineage 10) and cc32 (lineage 5).
Individual sequence types are not shown. From the total of 15,711 N. meningitidis genomes available from PubMLST as of
May 2019, each isolate was randomly chosen with a probability of 0.05, resulting in a total of 762 genomes. Allelic distance
profiles were loaded into SplitsTree4 (REF.152), and the Neighbor-Net algorithm151 was applied. The scale bar corresponds to
an allelic distance of 1.0. The maximum distance between any two isolates in an MLST comparison is seven. Unique lineage
11 sequence types are indicated by boxes. b | Neighbor-Net network of lineage 11 obtained with MLST data. MLST can
resolve phylogenetic relationships to the clonal complex level, but the lack of discriminatory power becomes apparent
when one is looking within a single clonal complex. Although this network consists of 193 isolates, only 12 distinct
genotypes were found. One hundred and eight-two of the isolates have an identical genotype and are located on the
central node. Isolates are annotated by serogroup. c | Neighbor-Net network of lineage 11 obtained by core genome
MLST (cgMLST). Whole-genome sequencing drastically increases the resolution of the phylogenetic network. This figure
was made with the 1,605 loci defined in the PubMLST core genome MLST scheme. In this scheme, all 193 strains have
unique genotypes, and it becomes evident that isolates cluster by serogroup.
Nature reviews
|
Microbiology
Reviews
than virulence-associated or antigen-encoding genes;
thus, evasion of host immune responses is unlikely to
explain the emergence of the epidemic waves in Africa59.
Whether changes in metabolic genes leading to small
differences in transmission fitness have a major role
in explaining changes in epidemic clones needs to be
confirmed for other hypervirulent lineages.
Lineage 5 (previously designated as the ST-32/ET-5
clonal complex) has been responsible for serogroup B
outbreaks globally for more than 40 years. Major epi-
demics were recorded in Norway, Cuba, Chile and
Brazil in the 1980s and 1990s, and prolonged outbreaks
were recorded in the Pacific Northwest of the USA
and in Normandy, France35,60,61. In contrast to lineages
11 and 3, similar or closely related clones of lineage 5
may express very different major antigenic proteins.
Analysis of the core genome of a small but global col-
lection of lineage 5 isolates revealed three distinct sub-
lineages — the ‘Asian group’ (sublineage 5.1), the ‘north
European–Norwegian group’, which contained isolates
with the PorA type P1.7, 16 (sublineage 5.2), and a ‘Latin
American group’ with PorA type P1.19, 15 (sublineage
5.3) — as well as several isolates which did not fall into
any of these groups. The most variable genes were those
encoding surface-exposed lipoproteins associated with
iron acquisition62.
As generation and analysis of WGS data is now
rapid and relatively inexpensive, WGS offers power-
ful opportunities for enhanced molecular surveillance
and is being established as a routine technique for
epidemiological studies of large meningococcal strain
collections. The Meningitis Research Foundation
Meningococcus Genome Library (MRF-MGL) was the
first genome-based initiative to make sequence data
from strains collected in the UK readily available63.
Starting in 2009, the MRF-MGL now includes more
than 4,000 sequenced isolates, and the isolate informa-
tion is deposited in the Neisseria PubMLST database.
A representative European meningococcal strain col-
lection of 799 IMD isolates from the epidemiological
year from July 2011 to June 2012 was also put together
and whole genome sequenced64. In addition to allowing
tracking of the pathogen and assessment of virulence
and antimicrobial resistance, such genome libraries are
especially valuable to document potential vaccine cov-
erage and to demonstrate the impact of non-capsular
vaccines65 (BOX1).
Carriage versus disease
Hyperinvasive lineages can be isolated from the oro-
pharynx of healthy carriers. Their prevalence in carriage
studies differs substantially, probably as a result of differ-
ent virulence potential and duration of colonization66,67.
Except for very rare cases, usually in immunocom-
promised individuals, disease-causing meningococci
are encapsulated, whereas isolates recovered from cul-
ture of oropharyngeal swabs often do not harbour, or
express only at low levels, a polysaccharide capsule66–68.
Absence or decreased expression of capsule is seen in
meningococci of identical genotypes recovered from
the nasopharynx compared with the invasive isolate in
individual patients69. The loss of capsule, which may
result from downregulation of capsule gene expression,
phase variation in the capsule synthesis genes (see later)
or inactivation of genes in the capsule gene cluster
(cps), is crucial in meningococcal biology, as intimate
adhesion on human mucosal surfaces and formation of
microcolonies can then be mediated by type IV pili69.
cps has been identified as a spontaneous point muta-
tion hotspot, and many carriage isolates do not possess
a complete capsule operon70,71. In some instances, the
genetic inability of strains to produce a capsule is a con-
sequence of a lack of the cps operon. In capsule-null
strains, the cps operon is replaced by a non-coding
region (cnl region)69,71. cnl-carrying meningococci have
been described in various lineages71–73, but with rare
exception74 disease caused by such strains occurs only
in immunocompromised individuals. Comparative
genome sequencing has been used in an attempt to dis-
cover other potential differences between carried and
invasive isolates. A study looking at genetic differences
between serogroup A isolates from carriers and patients
with IMD during an epidemic in Chad provided no
evidence of consistent differences between the carried
and invasive isolates75. A study performed in the course
of the serogroup B epidemic in New Zealand compared
the whole genomes of 12 throat isolates recovered from
household contacts of seven patients with the genome
of the index strain76. Within a household, isolates of the
same ST differed from the index strain by between 9
and 210 single-locus polymorphisms after exclusion of
Box 2 | Neisseria meningitidis as a cause of urethritis
N. meningitidis and Neisseria gonorrhoeae conventionally colonize distinct ecological
niches — the mucosa of the oronasopharynx and that of the genital tract, respectively;
however, there is overlap. The first report of isolation of N. meningitidis from the urogenital
tract dates from 1933 (REF.136), and isolation of the meningococcus from the cervix, urethra
or anal canal started to increase in the 1970s137. Sexual practices of men who have sex with
men were hypothesized as an important factor for transmission. Orogenital transmission
was first confirmed when the same C:2a:P1.5 strain was isolated from a patient’s urethral
exudates and from his sexual partner’s pharynx using pulsed-field gel electrophoresis for
genotyping138. In the past 5 years, there have been increasing reports of N. meningitidis as
the exclusive cause of symptomatic urethritis. A case caused by a serogroup W of the
sequence type 11 clonal complex was reported in Japan in 2013 from an HIV-positive
man139. During 2015, outbreaks of N. meningitidis urethritis emerged in several cities in
the USA. In all cases, isolates were non-encapsulated and typed as sequence type 11
(REFS52,140,141). Surprisingly, the clone emerged primarily among heterosexual men and
represented a new clade of lineage 11.2. The strain had adapted to the urogenital
environment by deletion of the capsule through insertion of IS1301 in the capsule operon,
enhancing mucosal adherence, and by acquisition of the gonococcal denitrification
pathway, promoting anaerobic growth141.
The strain evolved from a common ancestor that likely existed in 2011 (REF.54). One
study showed that a wide range of meningococcal genotypes have the ability to cause
urethritis142. Further, urethritis isolates of the same clade of clonal complex 11 were
recovered from men who have sex with men in Germany and France143. The gene
encoding factor H-binding protein (fHbp), which binds human factor H, a negative
complement regulator leading to enhanced survival in blood, had a premature stop
codon in all urethritis isolates, similarly to the non-functional homologue of fHbp found
in N. gonorrhoeae.
N. meningitidis urethritis raises major public health issues as urogenital diagnostic
methods usually do not encompass the meningococcus. Because nucleic acid
amplification tests are most frequently used for rapid diagnosis of gonorrhoea, such
meningococcal urogenital cases may also be unreported if further investigatory
tests are not performed144. Potential acquisition of antimicrobial resistance from the
gonococcus by horizontal gene transfer is an additional concern145.
www.nature.com/nrmicro
Reviews
pilS antigenic variation and predicted tandem repeats.
Of 94 variants found to cause amino acid substitutions,
insertions or deletions, only five were predicted to alter
protein function. These were in lgtC which encodes a
glycosyltransferase, a gene that encodes a chloride trans-
porter, hmbR which encodes a TonB-dependent haemo-
globin receptor, tbpA which encodes transferrin-binding
protein A and a gene encoding a citrate transporter
family protein76. On a similar note, the genomes of
capsulated invasive isolates and both capsulated and
non-capsulated isolates from asymptomatic carriers
from the lineage 5 outbreak in Normandy, France,
were compared using a gene-by-gene analysis77. Genes
involved in iron acquisition differed between the capsu-
lated invasive and carrier isolates, in particular the hmbR
gene, was switched off in capsulated carriage isolates77.
Population structure
Transformation and homologous recombination
have a major role in the genome plasticity and viru-
lence of meningococci78. The meningococcus relies
on sequence diversification to produce a surplus of
variants that might provide increased fitness and sur-
vival in a changing environment, allowing survival of
a bacterial subpopulation that is able to avoid the host
immune defences. Sequence diversity accumulates rap-
idly, largely as a consequence of recombination between
different lineages of the species during the carriage state
or with other related species colonizing the oral mucosa.
In experimental transformation, imported sequences
were found to be longer in the recipient if the genomic
DNA is derived from an intraspecies donor versus an
interspecies donor79. Uptake of foreign DNA from other
meningococcal strains and closely related species (that
is, the gonococcus and Neisseria lactamica) is facilitated
by the presence of ~2,000 copies of DNA uptake sequences
throughout the meningococcal genome80, whereas dis-
tinct variants of DNA uptake sequences found in other
members of the Neisseriaceae are efficient barriers to
interspecies recombination81.
Although the meningococcus has a highly dynamic
population structure as a result of horizontal gene trans-
fer, isolates can still be readily grouped into clonal com-
plexes or lineages owing to their similarity to a central
allelic profile. The diversity is limited by purification
events resulting from bottlenecks during transmission of
the bacteria to new geographical areas. This is suggested
by the strong geographical structuring observed in the
genomic diversity of lineages 5 and 11 (REFS40,62). Collapse
of the genomic diversity within ST-2859 of lineage 10
was demonstrated in a systematic longitudinal study of
meningococcal carriage and disease isolates collected
over a period of more than 10 years in northern Ghana82.
After a gap of 2 years, when the clone was displaced by a
serogroup W strain, ST-2859 meningococci reemerged,
both as a colonizer and as a meningitis-causing agent.
A profound reduction in genomic diversity among iso-
lates of the second wave was observed, with the expand-
ing new clone differing in only one single-nucleotide
poly morphism in a gene encoding the conserved
hypo thetical integral membrane protein NMAA_141
from some isolates of the original ST-2859 population,
astriking example of how genomic diversity of an epi-
demic clone can collapse when passing through a popu-
lation bottle neck82. Models of the population structure
for this highly recombining species have been debated
since 1993, when an epidemic population model was
proposed83 in which occasional clonal propagation of
highly fit organisms occurs in a predominantly recom-
bining population structure. More recently, a model of
predominantly clonal evolution, with restrained recom-
bination, has been suggested to better fit the newer
genetic data84. Bottlenecks82 and founder events resulting
from the spread of a few organisms to new geographical
areas85,86 have the most substantial role in the periodic
decreased diversity of the species.
Phase variation
Phase variation is a feature of certain host-adapted
pathogens, such as N. meningitidis, regulating a high-
frequency stochastic, reversible switching of gene
expression. Phase variation allows rapid changes in the
bacterium when it encounters a hostile host environ-
ment. The N. meningitidis pan-genome harbours more
than 100 genes that undergo phase variation by expan-
sion or contraction of simple sequence repeats, allowing
the switching of gene expression between on and off
states87. Each meningococcal isolate carries on average
more than 4,000 simple sequence repeats in its genome,
with each repeat unit usually being between one and
ten nucleotides in length87. Changes in the number of
repeats within a coding sequence can alter translation
by introducing frameshifts in the reading frame, and in
the proximity of a promoter, it can modulate transcrip-
tion. Rates of phase variation are often several orders
of magnitude greater than basal mutation rates, and
the frequency of switching is, in part, determined by the
number of repeats in the repeat tract88. In an analy-
sis using 78 complete or partial genome sequences of
N. meningitidis, a mean of 47 phase-variable genes per
genome was calculated89. Phase-variable genes include
virulence factors such as those involved in capsule
biosynthesis, restriction-modification systems, meta-
bolic proteins, bacteriocins and surface-expressed pro-
teins, such as pili glycosylation or modulation proteins,
adhesins and lipopolysaccharides87–92. Iron acquisition
systems that enable the meningococcus to acquire iron
from various iron-binding proteins within the human
host are particularly prone to phase variation93,94. The
TonB-dependent surface receptors HmbR and HpuAB
both undergo phase variation owing to poly(G) tracts
in the open reading frame of the genes95. Phase varia-
tion frequencies are controlled by a number of genetic
factors, including genes of the mismatch excision repair
and other DNA-repair pathways78,96,97.
The importance of phase variation in relation to
disease occurrence was recently illustrated in a study
which assessed phase variation in 737 UK serogroup
W invasive and carriage isolates of lineage 11 analysed
by WGS98. A selection of phase-variable genes encoding
outer membrane proteins were compared between the
original UK strain and the UK 2013 strain40. Statistically
significant increases in repeat number were detected in
the UK 2013 strain in genes encoding PorA, NadA and
DNA uptake sequences
Small repeated sequences
that are required for DNA
binding or uptake in natural
transformation in members
of the genus Neisseria.
Pan-genome
The sum of genes that are
found in at least one strain
of a species or population.
In addition to the core genome,
this includes the accessory
genome, which contains
dispensable genes present
in a subset of the strains.
Simple sequence repeats
DNA tracts in which a short
base pair motif is repeated
several times, which can be
found within the open reading
frame or within the promoter
region of a gene.
Nature reviews
|
Microbiology
Reviews
two opacity proteins, OpaD and OpaJ. Invasive and car-
riage isolates exhibited similar repeat numbers but the
absence of pilC expression was frequently associated
with disease. It was speculated that the rapid expansion
of the UK 2013 strain was due to a higher phase variation
rate, allowing it to avoid the immune response of the
host during transmission and consequently resulting in
an increased number of disease cases98.
Restriction modification and epigenetics
Restriction-modification activity consists of methyl-
ation of a specific DNA sequence by a methyltransferase
and cleavage of unmethylated DNA by a restriction
endonuclease (FIG.4). Such mechanisms are found in
all bacteria, but are particularly prevalent in naturally
competent organisms such as N. meningitidis99,100.
These systems are assumed to protect the bacterium
against infections by foreign DNA and may result in
sexual isolation99. All N. meningitidis strains possess
type III restriction-modification systems, with modi-
fication enzymes encoded by mod genes101. The pro-
tein Mod catalyses the methylation of a single strand
of DNA at a specific 4–6-bp region recognized by its
DNA recognition domain. Three phase-variable DNA
methyltransferases (ModA, ModB and ModD), which
mediate epigenetic regulation of distinct phase-variable
regulons (phasevarions), have been identified in
N.meningitidis102. Variable expression of methyltrans-
ferases leads to variable genome-wide methylation
differences and altered expression of multiple genes
through epigenetic mechanisms103. An investigation of
the distribution of mod genes and alleles in a collection
of 1,689 meningococcal genomes showed that modA
was present inall isolates, whereas modB and modD
were present in 78% and 25% of the isolates, respec-
tively104. Each mod gene has distinct alleles, defined by
their DNA recognition domain. modA alleles A12 and
A11 predominated (identified in 70% and 27.5% of the
isolates, respectively), whereas modB2 and modB1 were
the most common modB alleles (found in 49% and 42%
of themodB-positive isolates, respectively) and 75% of
the positive modD isolates had the allele modD1 (REF.104).
Astrong association with distinct meningococcal line-
ages was observed, although the dominant alleles were
found in multiple lineages. The modD1 phasevarion,
which alters resistance to oxidative stress101, was found
to be associated with hypervirulentlineages104.
These different alleles of the mod genes target and
methylate different DNA sequences, thereby regulat-
ing distinct gene sets. Phase variation of modA11 pro-
duced moderate (an average of twofold) alterations in
the expression of 285 genes, including those encoding
immunogenic outer membrane proteins such as the
lactoferrin-binding proteins, and also modulates DNA
repair and antibiotic sensitivity, while modA12 differ-
entially regulated 26 genes, some of them also involved
in iron acquisition105–107. Thus, with up to three inde-
pendently switching on or off mod genes, N. meningitidis
has a powerful epigenetic mechanism available to sto-
chastically vary gene expression and permit adaptation
in response to the highly selective immune pressure of
the host environment.
mod res
a
b
mod res
I
TRDR motif IV
c
Mod–Mod
Mod–Res
DNA DNA
Fig. 4 | Restriction-modification systems in Neisseria meningitidis. Briefly ,
restriction-modification systems work to protect the cell against foreign DNA
by cleavage at specific motifs, as mediated by restriction endonuclease genes,
with protection of self through the methylation of these same motifs mediated
by methyltransferase genes. a | Overview of type III restriction-modification
systems in N. meningitidis. The system consists of two genes; the methyltransferase
(modification) gene (mod) and the restriction endonuclease gene (res). Three
different mod genes have been described in N. meningitidis: modA, modB and
modD105. The three genes occupy different loci and do not display substantial
sequence similarity intheir functional domains. The modA gene is found in all
N. meningitidis isolates sequenced to date, modB is found in 78% and modD is found
in 25%104. A single mod gene contains an amino-terminal tetranucleotide (modA)
or pentanucleotide (modB and modD) repeat that is subject to phase variation (R).
Towards the centre of the gene, a variable target recognition domain (TRD) is
located, and this region determines the site of recognition and methylation.
The TRD is flanked on each side by conserved active site sequences DPPY (motif IV)
and FxGxG (also called motif I). b | Evolution of N. meningitidis with ample
recombination, interrupted by the invasion of a novel restriction-modification
system, which prevents further recombination and drives the evolution of a new ,
red lineage. The restriction-modification system is absent in the blue lineage, as
indicated by the dotted boxes. The mod and res genes produce Mod and Res proteins,
subunits of the functional enzyme complexes that perform the methyltransferase
and restriction endonuclease tasks. c | In the DNA of the red bacterium, the specific
recognition site (dark green) for the TRD has been methylated (light green triangle) by
an enzyme complex of two Mod subunits (light green circle sector), protecting it from
self-cleavage. In the blue bacterium, the equivalent recognition site is not methylated
(the dotted triangle representing absent methylation) since it has not acquired this
particular restriction-modification system. The blue and red bacteria can both freely
recombine internally with other members of their respective lineages. However, the
blue bacterium cannot donate DNA containing the specific recognition site to the red
bacterium because unmethylated recognition sites are recognized and subsequently
cleaved in the red bacterium by an enzyme complex consisting of a Mod subunit
(lightgreen circle sector) and a Res subunit (red circle sector). Recognition of the
specific recognition site for both methylation and restriction is determined by
theTRD in the Mod subunit (light green circle sector). Part a adapted with permission
from REF.101 Seib, K. L., Jen, F. E., Scott, A. L., Tan, A. & Jennings, M. P. Phase variation
of DNA methyltransferases and the regulation of virulence and immune evasion in
the pathogenic Neisseria. Pathog. Dis. (2017) 75 ftx080, by permission of Oxford
University Press. Parts b and c adapted with permission from REF.153, Proceedings
of the National Academy of Sciences USA.
www.nature.com/nrmicro
Reviews
Glycosylation
Glycosylation of proteins is a post-translational modifi-
cation associated with crucial biological processes impli-
cated in host–pathogen interactions108. N. meningitidis
exhibits a general O-linked protein glycosylation (pgl)
system in which several surface-exposed and periplas-
mic proteins are glycosylated109. Protein glycosylation
is important for protein function and interactions with
other microorganisms and host cells, and affects the
pathogenicity and virulence of the bacterium. The pgl
core locus encodes three enzymes (PglB, PglC and PglD)
involved in the synthesis of an undecaprenyl diphosphate
monosaccharide and three glycosyltranferases (PglA,
PglE and PglH) that can modify the monosaccharide by
addition of sugars. The disaccharide and trisaccharide
forms can be further modified through O-acetylation
mediated by PglI. PglF is responsible for translocation of
the glycan to the periplasmic side of the inner membrane,
and the PglO/PglL oligotransferase adds the sugar chain
onto the protein109,110. The pglA, pglE, pglH, and pglI genes
are phase variable, which results in the formation and
expression of multiple glycoforms. Although a variety of
glycosylated proteins has been identified in Neisseria spe-
cies, the PilE subunit of the pilin and the nitrate reductase
AniA are the best characterized neisserial glycoproteins111.
WGS has also revealed extensive polymorphism in the
pgl core locus, with a vari able presence of pglG (a putative
glycosyltransferase), pglH and pglI109,112,113. Homologous
recombination in the pgl loci was suggested to have a sub-
stantial role in the replacement of ST-7 by ST-2859 in the
meningitis belt of Africa. Compared with the ST-7 strains,
ST-2859 strains acquired a recombination block encom-
passing the pglD, pglC, pglB and pglH genes, whereas four
other independent recombination events affected this
locus in individual ST-2859 isolates58.
Within-host variation
WGS provides new means to investigate the genomic
evolution of bacteria during colonization and infection,
and in particular to study mechanisms of within-host
adaptation. Applying WGS to multiple isolates collected
from the same host is increasing our understanding of
the processes occurring during within-host evolution114.
To assess within-host genetic changes in isolates from
blood and the throat of four individuals with IMD,
ultradeep WGS (average coverage of 1,500-fold) was
performed on isolates recovered from both sites within
24 hours115. Eleven mutational events affecting eight
different loci (average of three events per isolate pair)
genetically separated the blood from the throat isolates
in each individual. These comprised eight slipped-strand
mispairing events and three recombinational events
due to gene conversion. The slipped-strand mispairing
events were located in pilC1 (three events), modA12
(two events), pglI, a phage-tail encoding gene and the
promoter of fetA (one event each), whereas the three
recombinational events included a Mu-like prophage, an
haemagglutinin-like adhesin and the major subunit of
the pilin protein, revealing that genes involved in type IV
pilus biogenesis were predominantly affected115. A com-
parison of paired blood and cerebrospinal isolates from
195 individuals with IMD showed that most pairs had
at least one variant locus between the two samples, again
with genes related to pilus biosynthesis being the most
frequently mutated116. Following infection with a lab-
oratory strain, several modifications of phase-variable
genes were detected after human passage, with porA,
lgtA, lgtC and hpuA being among the most affected117.
During long-term carriage, phase variation may reduce
the expression of genes that encode surface proteins to
avoid detection by the host immune system118. WGS
analyses of paired isolates from 50 individual menin-
gococcal carriers collected 2 months apart revealed
changes in genes belonging to the pilin family and the
restriction-modification systems and genes involved in
glycosylation119. Substantial changes in the pgl genotype
and/or glycan phenotype were identified in 48 of the
50 paired isolates113.
Virulence
The factors that determine whether invasive disease will
develop or not when a strain encounters a new host are yet
not completely understood. The variation in the rates of
IMD caused by different lineages suggests that the prop-
erties of the bacterium are essential, but the genetic basis
for the observed differences in virulence is still a matter
of investigation. Except for the genes involved in capsule
biosynthesis and a functional filamentous prophage (des-
ignated MDAΦ for ‘meningococcal disease-associated
island’) that has been associated with increased invasive-
ness120,121, most potential virulence genes identified in
meningococci are also present in other non-pathogenic
Neisseria species19 (FIG.5). Thus, it has been hypo thesized
that the propensity to cause disease is a multifactorial
property, depending on a combination of genetic ele-
ments that are commonly found in non-pathogenic spe-
cies122. When compared with the genomes of isolates from
individuals with IMD, similar isolates identified in the
throat of close contacts of the individuals were found to
harbour many differences, especially in genes known
to be phase variable76. Following transmission of one
or a few bacterial cells to a new host, the founder cells
will start to proliferate, and the stochastic assortment of
expressed virulence factors will produce a variant capable
of crossing the nasopharyngeal mucosa and invading the
bloodstream122. It has been suggested that hypervirulent
lineages differ not in their colonization ability but rather
in their ability to modulate the expression of genes, for
example those involved in the oxidative stress response
that allow dissemination within the host123. However,
acquisition by horizontal gene transfer of a functional
capsule locus and the MDAΦ prophage, which is known
to encode the immunoglobin-binding protein TspB124,
appears to be sufficient to transform an asymptomatic
carriage strain into a hypervirulent clone with potential
for causing large epidemics125.
Conclusions
WGS has made possible the exploration of the genome
of the highly variable species N. meningitidis in unprec-
edented detail. As a consequence, many new insights
have been gained during the past few years regarding
its origin, evolution, adaptation to the host and viru-
lence properties. Although there is compelling evidence
Nature reviews
|
Microbiology
Reviews
that N. meningitidis separated rather recently from
N. gonorrhoeae, the ecological separation between the
two species is becoming less clear. Increased contact
between the species, as a result of changing sexual atti-
tudes and practices, might have important public health
consequences, with concerns for diagnosis methods,
antimicrobial resistance development and treatment.
WGS has already become an invaluable tool for research-
ers studying Neisseria species, replacing other molecular
methods for surveillance and outbreak investigations.
MC58
Z2491
Nig8/13
DL13591
275
FAM18
DL20404
153
AR06000
14
KL11168
Virulence factor
Isolates
Capsule
BACY W CWEcnlNG X
pglB2
lgtG and lpxA
narE
lpxB
ctrG
lgtG
tonB
MDAφ phage
tspB
ctrABCDEF
pglI
pglGH
frpC
pglB
pan1
pilV
pglA
fetA
pglO
hmbR
recN, lpxA
Neisseria meningitidis diversity
2,632
0
1,000
2,000
Core genome
Locus position
Fig. 5 | Overview of the pan-genome content of 11 closed genomes of Neisseria meningitidis. The presence
(dark green) and absence (light green) of genes in 11 publicly available N. meningitidis genomes with different capsule
phenotypes (coloured boxes on the right side) is shown. Above the capsule annotations, a phylogenetic tree shows the
relation (as determined from the locus presence or absence patterns) between the isolates. In the outermost circle, known
virulence factors are annotated with red ticks. ‘Virulence factor’ here refers to any genetic element known to be central to
colonization, host invasion, immune system evasion or survival in adverse conditions such as in the presence of antibiotic
compounds. In the accessory genome, the names of these virulence factors are shown. Virulence factors in the core
genome are not annotated. They include a wide range of iron acquisition systems, invasins, efflux pumps, stress response
proteins, pilins, glycosylation systems, other adhesins and catalase. As for virulence factors in the accessory genome, they
include the capsule (including the capsule translocation system), the MDAΦ phage, hmbR- and fetA-mediated iron
acquisition, the frpC and narE toxin genes, lipooligosaccharide-related genes such as lgtG and lpxAB, as well as different
pilin glycosylation (pgl family) genes. The invasive isolates in this figure are FAM18, Z2491, MC58 and Nig8/13. There are
no single known virulence factors that clearly differentiate these invasive isolates from the non-invasive ones. The isolates
and the associated information (Neisseria PubMLST ID, serogroup, invasive or non-invasive infection and location) are as
follows: KL11168 (84412, serogroup X, non-invasive, Burkina Faso), 14 (30, non-groupable, non-invasive, Germany)154,
AR06000 (83698, serogroup null, non-invasive, Ethiopia), 153 (2077 , serogroup E, non-invasive, Germany)154, DL20404
(84413, serogroup W, non-invasive, Burkina Faso), FAM18 (698, serogroup C, invasive, USA)155, 275 (9756, serogroup W,
non-invasive, Germany)19, DL13591 (84387 , serogroup Y, non-invasive, Burkina Faso), Nig8/13 (21589, serogroup C,
invasive, Nigeria)125, Z2491 (613, serogroup A , invasive, The Gambia)156, and MC58 (240, serogroup B, invasive, UK)157.
These isolates were selected from publicly available closed genomes to represent a diverse range of serogroups.
www.nature.com/nrmicro
Reviews
The availability of large genome projects such as the
MRF-MGL and open-access Web-based databases such
as PubMLST allows in real time the detection and char-
acterization of outbreaks and refines our understand-
ing of global meningococcal epidemiology, as has been
illustrated by the analysis of lineage 11. The diversity
of the species is restricted by population bottlenecks
as well as by restriction-modification systems and
DNA uptake sequences, which might limit horizontal
gene transfer between lineages and species. Although
a few hypervirulent lineages have been responsible for
most of the IMD cases worldwide, the genetic proper-
ties that are required to cause disease are still not fully
established. The capsule is a prerequisite to IMD devel-
opment in almost all immunocompetent individuals
due to its antiphagocytic properties and by providing
resistance against complement-mediated killing. The
MDAΦ phage also appears to be important for disease
development, although its role and importance are still
subject to speculation. Many of the studies comparing
the genetic properties of isolates collected from different
types of clinical samples or with different disease status
identified the same genetic elements apparently under
selection pressure (that is, type IV pili, glycosylation pro-
teins, iron acquisition proteins, adhesins and evasins)
through an on/off regulation of expression by simple
sequence repeats. Further large-scale WGS studies are
clearly warranted to resolve conflicting results on which
virulence factors are essential for disease development
and how stochastic events on the mucosal membrane
can trigger pathogenicity. Improved and new technol-
ogies permitting analyses of bacterial genetic material
directly from clinical samples without the cultivation
step will also be essential. Stochastic variation affecting
expression of the large array of phase-variable genes may
be an important factor affecting invasion potential, but
further studies using deep sequencing are needed to
better assess which genetic factors or combinations of
factors have to be expressed for disease development.
Most currently generated WGS data are based on the
short-read Illumina sequencing technology. With WGS
used in combination with long-read sequencing, such as
Nanopore sequencing, which allows researchers to better
tackle sequence variation in the numerous repetitive ele-
ments present in N. meningitidis, questions regarding the
evolution and epidemiology can be further elucidated.
WGS has proved valuable in the development of vaccines
against serogroup B disease (BOX1) and is now the most
efficient way to determine potential coverage of these
protein-based vaccines, as well as to assess the changing
prevalence of vaccine antigens in the meningococcal
populations following vaccine introduction.
Published online xx xx xxxx
1. Christensen, H., May, M., Bowen, L., Hickman, M.
& Trotter, C. L. Meningococcal carriage by age:
a systematic review and meta-analysis. Lancet Infect.
Dis. 10, 853–861 (2010).
2. Cimolai, N. & Caugant D. A. in Laboratory Diagnosis
of Bacterial Infections (ed. Cimolai N.) 499–525
(Marcel Dekker, 2001).
3. Gotschlich, E. C., Goldschneider, I. & Artenstein, M. S.
Human immunity to the meningococcus. IV.
Immunogenicit y of group A and group C meningococcal
polysaccharides in human volunteers. J. Exp. Med.
129, 1367–1384 (1969).
4. Artenstein, M. S. etal. Prevention of meningococcal
disease by group C polysaccharide vaccines. N. Engl.
J. Med. 282, 417–420 (1970).
5. Jafri, R. Z. etal. Global epidemiology of invasive
meningococcal disease. Popul. Health Metr. 11, 17
(2013).
6. Wang, B., Santoreneos, R., Giles, L., Haji Ali Afzali, H.
& Marshall, H. Case fatality rates of invasive
meningococcal disease by serogroup and age:
a systematic review and meta-analysis. Vaccine 37,
2768–2782 (2019).
7. Stephens, D. S., Greenwood, B. & Brandtzaeg, P.
Epidemic meningitis, meningococcaemia, and Neisseria
meningitidis. Lancet 369, 2196–2210 (2007).
8. Vyse, A., Anonychuk, A., Jäkel, A., Wieffer, H. &
Nadel, S. The burden and impact of severe and
long-term sequelae of meningococcal disease.
Expert Rev. Anti Infect. Ther. 11, 597–604 (2013).
9. Jyssum, K. & Jyssum, S. Variation in density and
transformation potential in deoxyribonucleic acid from
Neisseria meningitidis. J. Bacteriol. 90, 1513–1519
(1965).
10. Feil, E. J., Maiden, M. C., Achtman, M. & Spratt, B. G.
The relative contributions of recombination and
mutation to the divergence of clones of Neisseria
meningitidis. Mol. Biol. Evol. 16, 1496–1502
(1999).
11. Vogel, U. & Frosch, M. The genus Neisseria: population
structure, genome plasticity, and evolution of
pathogenicity. Curr. Top. Microbiol. Immunol. 264,
23–45 (2002).
12. Liu, G., Tang, C. M. & Exley, R. M. Non-pathogenic
Neisseria: members of an abundant, multi-habitat,
diverse genus. Microbiology 161, 1297–1312
(2015).
13. Linz, B., Schenker, M., Zhu, P. & Achtman, M.
Frequent interspecific genetic exchange between
commensal Neisseriae and Neisseria meningitidis.
Mol. Microbiol. 36, 1049–1058 (2000).
14. Lu, Q. F. etal. Genus-wide comparative genomics
analysis of Neisseria to identify new genes associated
with pathogenicity and niche adaptation of Neisseria
pathogens. Int. J. Genomics 2019, 6015730 (2019).
15. Bennett, J. S., Watkins, E. R., Jolley, K. A.,
Harrison, O. B. & Maiden, M. C. Identifying Neisseria
species by use of the 50S ribosomal protein L6 (rplF)
gene. J. Clin. Microbiol. 52, 1375–1381 (2014).
16. Maiden, M. C. & Harrison, O. B. Population and
functional genomics of Neisseria revealed with
gene-by-gene approaches. J. Clin. Microbiol. 54,
1949–1955 (2016).
17. Weyrich, L. S. etal. Neanderthal behaviour, diet, and
disease inferred from ancient DNA in dental calculus.
Nature 544, 357–361 (2017).
18. Eerkens, J. W. etal. A probable prehistoric case of
meningococcal disease from San Francisco Bay:
next generation sequencing of Neisseria meningitidis
from dental calculus and osteological evidence. Int. J.
Paleopathol. 22, 173–180 (2018).
19. Schoen, C. etal. Whole-genome comparison of disease
and carriage strains provides insights into virulence
evolution in Neisseria meningitidis. Proc. Natl Acad.
Sci. USA 105, 3473–3478 (2008).
20. Schielke, S., Frosch, M. & Kurzai, O. Virulence
determinants involved in differential host niche
adaptation of Neisseria meningitidis and Neisseria
gonorrhoeae. Med. Microbiol. Immunol. 199,
185–196 (2010).
21. Clemence, M. E. A., Maiden, M. C. J. & Harrison, O. B.
Characterization of capsule genes in non-pathogenic
Neisseria species. Microb. Genom. 4, e0.000208
(2018).
22. Lapeysonnie, L. La méningite cérébrospinale en
Afrique. Bull. World Health Organ. 28, 1–114
(1963).
23. Greenwood, B. Manson Lecture. Meningococcal
meningitis in Africa. Trans. R. Soc. Trop. Med. Hyg.
93, 341–353 (1999).
24. Stephens, D. S. Conquering the meningococcus.
FEMS Microbiol. Rev. 31, 3–14 (2007).
25. Harrison, O. B. etal. Description and nomenclature of
Neisseria meningitidis capsule locus. Emerg. Infect. Dis.
19, 566–573 (2013).
26. Tzeng, Y. L. & Stephens, D. S. Epidemiology and
pathogenesis of Neisseria meningitidis. Microbes
Infect. 2, 687–700 (2000).
27. Diomandé, F. V. Public health impact after the
introduction of PsA-TT: the first 4 years. Clin. Infect.
Dis. 61, S467–S472 (2015).
28. Borrow, R. etal. The Global Meningococcal Initiative:
global epidemiology, the impact of vaccines on
meningococcal disease and the importance of herd
protection. Expert Rev. Vaccines 16, 313–328
(2017).
29. Krauland, M. G. etal. Whole genome sequencing to
investigate the emergence of clonal complex 23
Neisseria meningitidis serogroup Y disease in the
United States. PLOS ONE 7, e35699 (2012).
30. Bröker, M. etal. Meningococcal serogroup Y disease
in Europe: continuation of high importance in some
European regions in 2013. Hum. Vaccin. Immunother.
11, 2281–2286 (2015).
31. Mayer, L. W. etal. Outbreak of W135 meningococcal
disease in 2000: not emergence of a new W135
strain but clonal expansion within the electophoretic
type-37 complex. J. Infect. Dis. 185, 1596–1605
(2002).
32. Koumaré, B. etal. The first large epidemic of
meningococcal disease caused by serogroup W135,
Burkina Faso, 2002. Vaccine 25, A37–A41 (2007).
33. Abad, R., López, E. L., Debbag, R. & Vázquez, J. A.
Serogroup W meningococcal disease: global spread
and current affect on the Southern Cone in Latin
America. Epidemiol. Infect. 142, 2461–2470 (2014).
34. Krone, M. etal. Increase of invasive meningococcal
serogroup W disease in Europe, 2013 to 2017.
Euro Surveill. 24, e2807 (2019).
35. Caugant, D. A. etal. Intercontinental spread of a
genetically distinctive complex of clones of Neisseria
meningitidis causing epidemic disease. Proc. Natl
Acad. Sci. USA 83, 4927–4931 (1986).
36. Olyhoek, T., Crowe, B. A. & Achtman, M. Clonal
population structure of Neisseria meningitidis
serogroup A isolated from epidemics and pandemics
between 1915 and 1983. Rev. Infect. Dis. 9,
665–692 (1987).
37. Maiden, M. C. etal. Multilocus sequence typing:
a portable approach to the identification of clones
within populations of pathogenic microorganisms.
Proc. Natl Acad. Sci. USA 95, 3140–3145 (1998).
38. Yazdankhah, S. P. etal. 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,
5146–5153 (2004).
Nature reviews
|
Microbiology
Reviews
39. Golparian, D. & Unemo, M. Will genome analysis
elucidate evolution, global transmission and virulence
of Neisseria meningitidis lineages? EBioMedicine 2,
186–187 (2015).
40. Lucidarme, J. etal. Genomic resolution of an
aggressive, widespread, diverse and expanding
meningococcal serogroup B, C and W lineage.
J. Infect. 71, 544–552 (2015).
This study demonstrates the power of whole
genome sequencing to elucidate the global
epidemiology of lineage 11.
41. Bratcher, H. B., Corton, C., Jolley, K. A., Parkhill, J.
& Maiden, M. C. A gene-by-gene population
genomics platform: denovo assembly, annotation
and genealogical analysis of 108 representative
Neisseria meningitidis genomes. BMC Genom. 15,
1138 (2014).
42. Topaz, N. etal. Phylogenetic relationships and
regional spread of meningococcal strains in the
meningitis belt, 2011–2016. EBioMedicine 41,
488–496 (2019).
43. Jelfs, J., Munro, R., Ashton, F. E. & Caugant, D. A.
Genetic characterization of a new variant within the
ET-37 complex of Neisseria meningitidis associated
with outbreaks in various parts of the world.
Epidemiol. Infect. 125, 285–298 (2000).
44. Ramsay, M. E., Andrews, N., Kaczmarski, E. B. &
Miller, E. Efficacy of meningococcal serogroup C
conjugate vaccine in teenagers and toddlers in
England. Lancet 357, 195–196 (2001).
45. Retchless, A. C. etal. The establishment and
diversification of epidemic-associated serogroup W
meningococcus in the African meningitis belt,
1994–2012. mSphere 1, e00201–e00216
(2016).
46. Mustapha, M. M. etal. Genomic epidemiology
of hypervirulent serogroup W, ST-11 Neisseria
meningitidis. EBioMedicine 2, 1447–1455 (2015).
47. Mowlaboccus, S. etal. Clonal expansion of a new
penicillin-resistant clade of Neisseria meningitidis
serogroup W clonal complex 11, Australia. Emerg.
Infect. Dis. 23, 1364–1367 (2017).
48. Lucidarme, J. An international invasive meningococcal
disease outbreak due to a novel and rapidly
expanding serogroup W strain, Scotland and Sweden,
July to August 2015. Euro Surveill. 21, 30395
(2016).
49. Eriksson, L. etal. Whole-genome sequencing of
emerging invasive Neisseria meningitidis serogroup W
in Sweden. J. Clin. Microbiol. 56, e01409–e01417
(2018).
50. Taha, M.-K., Deghmane, A. E., Knol, M. &
vander Ende, A. Whole genome sequencing reveals
Trans-European spread of an epidemic Neisseria
meningitidis serogroup W clone. Clin. Microbiol. Infect.
25, 765–767 (2019).
51. Campbell, H., etal. Presentation with gastrointestinal
symptoms and high case fatality associated with group
W meningococcal disease (MenW) in teenagers,
England, July 2015 to January 2016. Euro Surveill.
21, 30175 (2016).
52. Tzeng, Y. L. etal. Emergence of a new Neisseria
meningitidis clonal complex 11 lineage 11.2 clade as
an effective urogenital pathogen. Proc. Natl Acad.
Sci. USA 114, 4237–4242 (2017).
An emerging strain of N. meningitidis causing
urethritis in the United States adaptated to the
urogenital environment by loss of the capsule
and acquisition of the N. gonorrheae norB–aniA
cassette promoting anaerobic growth.
53. Kahler, C. M. Emergence of a urogenital pathotype
of Neisseria meningitidis. Trends Microbiol. 25,
510–512 (2017).
54. Retchless, A. C. etal. Expansion of a urethritis-
associated Neisseria meningitidis clade in the United
States with concurrent acquisition of N. gonorrhoeae
alleles. BMC Genom. 19, 176 (2018).
55. Moore, P. S., Reeves, M. W., Schwartz, B., Gellin, B. G.
& Broome, C. V. Intercontinental spread of an
epidemic group A Neisseria meningitidis strain.
Lancet 2, 260–263 (1989).
56. Morelli, G. etal. Clonal descent and microevolution
of Neisseria meningitidis during 30 years of epidemic
spread. Mol. Microbiol. 25, 1047–1064 (1997).
57. Caugant, D. A. etal. Molecular characterization of
invasive meningococcal isolates from countries in
the African meningitis belt before introduction of a
serogroup A conjugate vaccine. PLOS ONE 7, e46019
(2012).
58. Lamelas, A. etal. 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 5, e01974-14 (2014).
A genomic study showing the evolutionary changes
occurring during clonal replacement within a
serogroup A lineage in the African meningitis belt
and highlighting the role of protein glycosylation
for immune evasion.
59. Watkins, E. R. & Maiden, M. C. Metabolic shift in the
emergence of hyperinvasive pandemic meningococcal
lineages. Sci. Rep. 7, 41126 (2017).
60. Diermayer, M. etal. Epidemic serogroup B
meningococcal disease in Oregon: the evolving
epidemiology of the ET-5 strain. JAMA 281,
1493–1497 (1999).
61. Rouaud, P. etal. Prolonged outbreak of B
meningococcal disease in the Seine-Maritime
department, France, January 2003 to June 2005.
Euro Surveill. 11, 178–181 (2006).
62. Harrison, O. B., Bray, J. E., Maiden, M. C. &
Caugant, D. A. Genomic analysis of the evolution and
global spread of hyper-invasive meningococcal lineage
5. EBioMedicine 2, 234–243 (2015).
63. Hill, D. M. etal. Genomic epidemiology of
age-associated meningococcal lineages in national
surveillance: an observational cohort study. Lancet
Infect. Dis. 15, 1420–1428 (2015).
64. Bratcher, H. B. etal. Establishment of the European
meningococcal strain collection genome library
(EMSC-GL) for the 2011 to 2012 epidemiological year.
Euro Surveill. 23 (2018).
65. Brehony, C. etal. Distribution of Bexsero® antigen
sequence types (BASTs) in invasive meningococcal
disease isolates: implications for immunisation.
Vaccine 34, 4690–4697 (2016).
66. Yazdankhah, S. P. & Caugant, D. A. Neisseria
meningitidis: an overview of the carrier state.
J. Med. Microbiol. 53, 821–832 (2004).
67. Caugant, D. A., Tzanakaki, G. & Kriz, P. Lessons from
meningococcal carriage studies. FEMS Microbiol. Rev.
31, 52–63 (2007).
68. Jones, C. H. etal. Comparison of phenotypic and
genotypic approaches to capsule typing of Neisseria
meningitidis by use of invasive and carriage isolate
collections. J. Clin. Microbiol. 54, 25–34 (2016).
69. Tzeng, Y. L., Thomas, J. & Stephens, D. S. Regulation of
capsule in Neisseria meningitidis. Crit. Rev. Microbiol.
42, 759–772 (2016).
70. Ispasanie, E. etal. Spontaneous point mutations in
the capsule synthesis locus leading to structural and
functional changes of the capsule in serogroup A
meningococcal populations. Virulence 9, 1138–1149
(2018).
71. Claus, H., Maiden, M. C., Maag, R., Frosch, M. &
Vogel, U. Many carried meningococci lack the genes
required for capsule synthesis and transport.
Microbiology 148, 1813–1819 (2002).
72. Ganesh, K. etal. Molecular characterization of
invasive capsule null Neisseria meningitidis in
South Africa. BMC Microbiol. 17, 40 (2017).
73. Neri, A. etal. Carriage meningococcal isolates
with capsule null locus dominate among high
school students in a non-endemic period, Italy,
2012–2013. Int. J. Med. Microbiol. 309, 182–188
(2019).
74. Xu, Z., Zhu, B., Xu, L., Gao, Y. & Shao, Z. First case of
Neisseria meningitidis capsule null locus infection in
China. Infect. Dis. 47, 591–592 (2015).
75. Diallo, K. etal. Hierarchical genomic analysis of
carried and invasive serogroup A Neisseria
meningitidis during the 2011 epidemic in Chad.
BMC Genom. 18, 398 (2017).
76. Ren, X. etal. Genomic, transcriptomic, and phenotypic
analyses of Neisseria meningitidis isolates from
disease patients and their household contacts.
mSystems 2, e00127-17 (2017).
A comparison of closely related disease- and
carriage-associated meningococci using a
combination of genetic and phenotypic tools to
understand mechanisms associated with virulence.
77. Sevestre, J. etal. Differential expression of hemoglobin
receptor, HmbR, between carriage and invasive
isolates of Neisseria meningitidis contributes to
virulence: lessons from a clonal outbreak. Virulence 9,
923–929 (2018).
78. Davidsen, T. & Tønjum, T. Meningococcal genome
dynamics. Nat. Rev. Microbiol. 4, 11–22 (2006).
79. Alfsnes, K. etal. A genomic view of experimental
intraspecies and interspecies transformation of a
rifampicin-resistance allele into Neisseria meningitidis.
Microb. Genom. 4, e000222 (2018).
80. Ambur, O. H., Frye, S. A. & Tønjum, T. New functional
identity for the DNA uptake sequence in transformation
and its presence in transcriptional terminators.
J. Bacteriol. 189, 2077–2085 (2007).
81. Frye, S. A., Nilsen, M., Tønjum, T. & Ambur, O. H.
Dialects of the DNA uptake sequence in Neisseriaceae.
PLOS Genet. 9, e1003458 (2013).
82. Lamelas, A. etal. Loss of genomic diversity in a
Neisseria meningitidis clone through a colonization
bottleneck. Genome Biol. Evol. 10, 2102–2109
(2018).
83. Maynard Smith, J., Smith, N. H., O'Rourke, M. &
Spratt, B. G. How clonal are bacteria? Proc. Natl
Acad. Sci. USA 90, 4384–4388 (1993).
84. Tibayrenc, M. & Ayala, F. J. How clonal are Neisseria
species? The epidemic clonality model revisited.
Proc. Natl Acad. Sci. USA 112 , 8909–8913 (2015).
85. Achtman, M. & Wagner, M. Microbial diversity
and the genetic nature of microbial species. Nat. Rev.
Microbiol. 6, 431–440 (2008).
86. Zhu, P. etal. Fit genotypes and escape variants of
subgroup III Neisseria meningitidis during three
pandemics of epidemic meningitis. Proc. Natl Acad.
Sci. USA 98, 5234–5239 (2001).
87. Siena, E. etal. In-silico prediction and deep-DNA
sequencing validation indicate phase variation in 115
Neisseria meningitidis genes. BMC Genom. 17, 843
(2016).
88. Saunders, N. J. etal. Repeat-associated phase
variable genes in the complete genome sequence of
Neisseria meningitidis strain MC58. Mol. Microbiol.
37, 207–215 (2000).
89. Wanford, J. J., Green, L. R., Aidley, J. & Bayliss, C. D.
Phasome analysis of pathogenic and commensal
Neisseria species expands the known repertoire of
phase variable genes, and highlights common adaptive
strategies. PLOS ONE 13, e0196675 (2018).
90. Srikhanta, Y. N., Maguire, T. L., Stacey, K. J.,
Grimmond, S. M. & Jennings, M. P. The phasevarion:
a genetic system controlling coordinated, random
switching of expression of multiple genes. Proc. Natl
Acad. Sci. USA 102, 5547–5551 (2005).
91. Bayliss, C. D. etal. Neisseria meningitidis escape from
the bactericidal activity of a monoclonal antibody is
mediated by phase variation of lgtG and enhanced by
a mutator phenotype. Infect. Immun. 76, 5038–5048
(2008).
92. Green, L. R. etal. Phase variation of NadA in invasive
Neisseria meningitidis isolates impacts on coverage
estimates for 4C-MenB, a MenB vaccine. J. Clin.
Microbiol. 56, e00204 (2018).
93. Tauseef, I. etal. Influence of the combination and
phase variation status of the haemoglobin receptors
HmbR and HpuAB on meningococcal virulence.
Microbiology 157, 1446–1456 (2011).
94. Lucidarme, J. etal. The distribution and ‘in vivo’
phase variation status of haemoglobin receptors in
invasive meningococcal serogroup B disease:
genotypic and phenotypic analysis. PLOS ONE 8,
e76932 (2013).
95. Lewis, L. A. etal. Phase variation of HpuAB and HmbR,
two distinct haemoglobin receptors of Neisseria
meningitidis DNM2. Mol. Microbiol. 32, 977–989
(1999).
96. Richardson, A. R. & Stojiljkovic, I. Mismatch repair
and the regulation of phase variation in Neisseria
meningitidis. Mol. Microbiol. 40, 645–655 (2001).
97. Martin, P., Sun, L., Hood, D. W. & Moxon, E. R.
Involvement of genes of genome maintenance in the
regulation of phase variation frequencies in Neisseria
meningitidis. Microbiology 150, 3001–3012 (2004).
98. Green, L. R. etal. Potentiation of phase variation in
multiple outer membrane proteins during spread of
the hyperinvasive Neisseria meningitidis serogroup W
ST-11 lineage. J. Infect. Dis. 220, 1109–1117 (2019).
99. Bickle, T. A. & Krüger, D. H. Biology of DNA
restriction. Microbiol. Rev. 57, 434–450 (1993).
100. Atack, J. M., Yang, Y., Seib, K. L., Zhou, Y. &
Jennings, M. P. A survey of type III restriction-
modification systems reveals numerous, novel
epigenetic regulators controlling phase-variable
regulons; phasevarions. Nucleic Acids Res. 46,
3532–3542 (2018).
101. Seib, K. L., Jen, F. E., Scott, A. L., Tan, A. &
Jennings, M. P. Phase variation of DNA
methyltransferases and the regulation of virulence
and immune evasion in the pathogenic Neisseria.
Pathog. Dis. 75, ftx080 (2017).
A review describing the importance of epigenetic
changes mediated by phase variable DNA
methlytransferases in the pathogenic Neisseria
species.
102. Srikhanta, Y. N., Fox, K. L. & Jennings, M. P.
The phasevarion: phase variation of type III DNA
www.nature.com/nrmicro
Reviews
methyltransferases controls coordinated switching
in multiple genes. Nat. Rev. Microbiol. 8, 196–206
(2010).
103. Phillips, Z. N., Husna, A. U., Jennings, M. P., Seib, K. L.
& Atack, J. M. Phasevarions of bacterial pathogens -
phase-variable epigenetic regulators evolving from
restriction-modification systems. Microbiology 165,
917–928 (2019).
104. Tan, A. etal. Distribution of the type III DNA
methyltransferases modA, modB and modD among
Neisseria meningitidis genotypes: implications for gene
regulation and virulence. Sci. Rep. 6, 21015 (2016).
105. Srikhanta, Y. N. etal. Phasevarions mediate random
switching of gene expression in pathogenic Neisseria.
PLOS Pathog. 5, e1000400 (2009).
106. Jen, F. E., Seib, K. L. & Jennings, M. P. Phasevarions
mediate epigenetic regulation of antimicrobial
susceptibility in Neisseria meningitidis. Antimicrob.
Agents Chemother. 58, 4219–4221 (2014).
107. Seib, K. L. etal. Specificity of the ModA11, ModA12
and ModD1 epigenetic regulator N6-adenine DNA
methyltransferases of Neisseria meningitidis. Nucleic
Acids Res. 43, 4150–4162 (2015).
108. Bhat, A. H., Maity, S., Giri, K. & Ambatipudi, K.
Protein glycosylation: sweet or bitter for bacterial
pathogens? Crit. Rev. Microbiol. 45, 82–102 (2019).
109. Børud, B. etal. Extended glycan diversity in a
bacterial protein glycosylation system linked to
allelic polymorphisms and minimal genetic alterations
in a glycosyltransferase gene. Mol. Microbiol. 94,
688–699 (2014).
110 . Gault, J. etal. Neisseria meningitidis type IV pili
composed of sequence invariable pilins are masked by
multisite glycosylation. PLOS Pathog. 11, e1005162
(2015).
111. Mubaiwa, T. D., etal. The sweet side of the
pathogenic Neisseria: the role of glycan interactions
in colonisation and disease. Pathog. Dis. 75, ftx063
(2017).
112 . Børud, B. etal. Genetic and molecular analyses reveal
an evolutionary trajectory for glycan synthesis in a
bacterial protein glycosylation system. Proc. Natl
Acad. Sci. USA 108, 9643–9648 (2011).
113 . Børud, B., Bårnes, G. K., Brynildsrud, O. B.,
Fritzsønn, E. & Caugant, D. A. Genotypic and
phenotypic characterization of the O-linked protein
glycosylation system reveals high glycan diversity in
paired meningococcal carriage isolates. J. Bacteriol.
200, e00794–17 (2018).
114 . Didelot, X., Walker, A. S., Peto, T. E., Crook, D. W.
& Wilson, D. J. Within-host evolution of bacterial
pathogens. Nat. Rev. Microbiol. 14, 150–162 (2016).
115 . Klughammer, J. etal. Comparative genome sequencing
reveals within-host genetic changes in Neisseria
meningitidis during invasive disease. PLOS ONE 12,
e0169892 (2017).
An ultra-deep sequencing analysis of throat-blood
strain pairs isolated from four patients detected
mutations affecting predominantly contingency
genes involved in type IV pilus biogenesis.
116 . Lees, J. A. etal. Large scale genomic analysis shows
no evidence for pathogen adaptation between the
blood and cerebrospinal fluid niches during bacterial
meningitis. Microb. Genom. 3, e000103 (2017).
117 . Omer, H. etal. Genotypic and phenotypic modifications
of Neisseria meningitidis after an accidental human
passage. PLOS ONE 6, e17145 (2011).
118 . Alamro, M. etal. Phase variation mediates reductions
in expression of surface proteins during persistent
meningococcal carriage. Infect. Immun. 82,
2472–2484 (2014).
119 . Bårnes, G. K. etal. Whole genome sequencing reveals
within-host genetic changes in paired meningococcal
carriage isolates from Ethiopia. BMC Genom. 18, 407
(2017).
120. Bille, E. etal. A chromosomally integrated
bacteriophage in invasive meningococci. J. Exp. Med.
201, 1905–1913 (2005).
121. Bille, E. etal. Association of a bacteriophage with
meningococcal disease in young adults. PLOS ONE 3,
e3885 (2008).
122. Siena, E., Bodini, M. & Medini, D. Interplay between
virulence and variability factors as a potential driver
of invasive meningococcal disease. Comput. Struct.
Biotechnol. J. 16, 61–69 (2018).
This article supports the hypothesis that invasive
meningococcal disease arises from the ability
of the bacterium to develop phenotypic variants
through stochastic assortment of a repertoire
of virulence factors.
123. Schoen, C., Kischkies, L., Elias, J. & Ampattu, B. J.
Metabolism and virulence in Neisseria meningitidis.
Front. Cell. Infect. Microbiol. 4, 114 (2014).
124. Müller, M. G., Ing, J. Y., Cheng, M. K. W., Flitter, B. A.
& Moe, G. R. Identification of a phage encoded
Ig-binding protein from invasive Neisseria meningitidis.
J. Immunol. 191, 3287–3296 (2013).
125. Brynildsrud, O. B. etal. Acquisition of virulence genes
by a carrier strain gave rise to the ongoing epidemics
of meningococcal disease in West Africa. Proc. Natl
Acad. Sci. USA 115, 5510–5515 (2018).
A study showing how acquisition of a few virulence
genes by a benign meningococcal carrier strain can
have major public health consequences.
126. Dull, P. M. & McIntosh, E. D. Meningococcal vaccine
development – from glycoconjugates against
MenACWY to proteins against MenB – potential
for broad protection against meningococcal disease.
Vaccine 30, B18–B25 (2012).
127. Vella, M. & Pace, D. Glycoconjugate vaccines:
an update. Expert Opin. Biol. Ther. 15, 529–546
(2015).
128. Chen, W. H. etal. Safety and immunogenicity of a
pentavalent meningococcal conjugate vaccine
containing serogroups A, C, Y, W, and X in healthy
adults: a phase 1, single-centre, double-blind,
randomised, controlled study. Lancet Infect. Dis. 18,
1088–1096 (2018).
129. Christodoulides, M. & Heckels, J. Novel approaches
to Neisseria meningitidis vaccine design. Pathog. Dis.
75, ftx033 (2017).
130. Sette, A. & Rappuoli, R. Reverse vaccinology:
developing vaccines in the era of genomics. Immunity
33, 530–541 (2010).
131. Rappuoli, R., Pizza, M., Masignani, V. & Vadivelu, K.
Meningococcal B vaccine (4CMenB): the journey from
research to real world experience. Expert Rev.
Vaccines 17, 1111–1121 (2018).
132. Murphy, E. etal. Sequence diversity of the factor H
binding protein vaccine candidate in epidemiologically
relevant strains of serogroup B Neisseria meningitidis.
J. Infect. Dis. 200, 379–389 (2009).
133. Perez, J. L. etal. From research to licensure and
beyond: clinical development of MenB-FHbp, a
broadly protective meningococcal B vaccine. Expert
Rev. Vaccines 17, 461–477 (2018).
134. Hoiseth, S. K. etal. A multi-country evaluation of
Neisseria meningitidis serogroup B factor H-binding
proteins and implications for vaccine coverage in
different age groups. Pediatr. Infect. Dis. J. 32,
1096–1101 (2013).
135. Rodrigues, C. M. C. etal. Genomic surveillance
of 4CMenB vaccine antigenic variants among
disease-causing Neisseria meningitidis isolates,
United Kingdom, 2010–2016. Emerg. Infect. Dis. 24,
673–682 (2018).
136. Murray, E. G. D. Meningococcus infection of the male
urogenital tract and the liability to confusuion with
gonococcus infection. Urol. Cutan. Rev. 43, 739–741
(1939).
137. Givan, K. F., Thomas, B. W. & Johnston, A. G. Isolation
of Neisseria meningitidis from the urethra, cervix, and
anal canal: further observations. Br. J. Vener. Dis. 53,
109–112 (1977).
138. Urra, E. etal. Orogenital transmission of Neisseria
meningitidis serogroup C confirmed by genotyping
techniques. Eur. J. Clin. Microbiol. Infect. Dis. 24,
51–53 (2005).
139. Ito, S. etal. Male non-gonococcal urethritis: from
microbiological etiologies to demographic and clinical
features. Int. J. Urol. 23, 325–331 (2016).
140. Bazan, J. A. etal. Large cluster of Neisseria
meningitidis urethritis in Columbus, Ohio, 2015.
Clin. Infect. Dis. 65, 92–99 (2017).
141. Toh, E. etal. Neisseria meningitidis ST11 complex
isolates associated with nongonococcal urethritis,
Indiana, USA, 2015–2016. Emerg. Infect. Dis. 23,
336–339 (2017).
142. Ma, K. C. etal. Genomic characterization of
urethritis-associated Neisseria meningitidis shows that
a wide range of N. meningitidis strains can cause
urethritis. J. Clin. Microbiol. 55, 3374–3383 (2017).
143. Taha, M. K. etal. Evolutionary events associated
with an outbreak of meningococcal disease in men
who have sex with men. PLOS ONE 11, e0154047
(2016).
144. Genders, R. E., Spitaels, D., Jansen, C. L., van den
Akker, T. W. & Quint, K. D. A misleading urethral
smear with polymorphonuclear leucocytes and
intracellular diplococci; case report of urethritis
caused by Neisseria meningitidis. J. Med. Microbiol.
62, 1905–1906 (2013).
145. Tzeng, Y. L. etal. Heteroresistance to the model
antimicrobial peptide polymyxin B in the emerging
Neisseria meningitidis lineage 11.2 urethritis clade:
mutations in the pilMNOPQ operon. Mol. Microbiol.
111, 254–268 (2019).
146. Hill, D. J., Griffiths, N. J., Borodina, E. & Virji, M.
Cellular and molecular biology of Neisseria
meningitidis colonization and invasive disease.
Clin. Sci. 118 , 547–564 (2010).
147. Massari, P. etal. Cutting edge: immune stimulation
by neisserial porins is Toll-like receptor 2 and
MyD88 dependent. J. Immunol. 168, 1533–1537
(2002).
148. Woodhams, K. L., Chan, J. M., Lenz, J. D., Hackett, K. T.
& Dillard, J. P. Peptidoglycan fragment release from
Neisseria meningitidis. Infect. Immun. 81, 3490–3498
(2013).
149. Bennett, J. S. etal. A genomic approach to bacterial
taxonomy: an examination and proposed reclassification
of species within the genus Neisseria. Microbiology
158, 1570–1580 (2012).
150. Katoh, K. & Standley, M. MAFFT multiple sequence
alignment software version 7: improvements in
performance and usability. Mol. Biol. Evol. 30,
772–780 (2013).
151. Bryant, D. & Moulton, V. Neighbor-Net: an
agglomerative method for the construction of
phylogenetic networks. Mol. Biol. Evol. 21, 255–265
(2004).
152. Huson, D. H. & Bryant, D. User manual for SplitsTree4
V4. 13.1. (2010).
153. Budroni, S. etal. Neisseria meningitidis is structured
in clades associated with restriction modification
systems that modulate homologous recombination.
Proc. Natl Acad. Sci. USA 108, 4494–4499 (2011).
154. Claus, H. etal. Genetic analysis of meningococci
carried by children and young adults. J. Infect. Dis.
191, 1263–1271 (2005).
155. Bentley, S. D. etal. Meningococcal genetic variation
mechanisms viewed through comparative analysis
of serogroup C strain FAM18. PLOS Genet. 3, e23
(2007).
156. Parkhill, J. etal. Complete DNA sequence of a
serogroup A strain of Neisseria meningitidis Z2491.
Nature 404, 502–506 (2000).
157. Tettelin, H. etal. Complete genome sequence of
Neisseria meningitidis serogroup B strain MC58.
Science 287, 1809–1815 (2000).
Author contributions
The authors contributed equally to all aspects of the article.
Competing interests
The authors declare no competing interests.
Peer review information
Nature Reviews Microbiology thanks C. D. Bayliss, D. S. Stephens
and the other, anonymous, reviewer(s) for their contribution
to the peer review of this work.
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional
claims in published maps and institutional affiliations.
RELATED LINKS
Neisseria PubMLST database: https://pubmlst.org/neisseria/
Nature reviews
|
Microbiology
Reviews
