riage. Nevertheless, shifts in colonization and disease to-
ward nonvaccine serotypes and other potential pathogens
have been described. To understand the extent of these
shifts,? we? analyzed? nasopharyngeal? microbial? profiles? of?
ticipating in a randomized controlled trial in the Nether-
microbial community composition and increased bacterial
diversity. Immunization also resulted in decreased presence
of the pneumococcal vaccine serotype and an increase in
the relative abundance and presence of nonpneumococ-
abundance of Haemophilus and Staphylococcus bacteria in
vaccinees was increased over that in controls. This study
highlights the need for careful monitoring when implement-
ing vaccines directed against common colonizers.
against a specific pathogen and by eradication of these spe-
cific pathogens from the population, leading to so called
herd effects or indirect protection (1). Over the past decade,
a 7-valent pneumococcal conjugate vaccine (PCV-7) was
accination is one of the most effective methods to pre-
vent infectious diseases by direct protection of persons
introduced in national immunization programs for newborns
in most high-income countries, and the newer-generation
10-valent and 13-valent vaccines are being progressively in-
troduced in developing countries (2).
The specific serotypes of the first licensed 7-valent
pneumococcal vaccine are common colonizers of the up-
per respiratory tract of children during the first years of
life, in which these serotypes generally reside as part of
the nasopharyngeal microbiota (bacterial community) (3).
However, these bacteria might occasionally spread be-
yond this niche and cause otitis media, pneumonia, sep-
sis, or meningitis (4). Vaccines show effectiveness against
vaccine-serotype disease, nasopharyngeal acquisition of
pneumococci, and pneumococcal transmission. However,
nonvaccine pneumoccal serotypes fill the vacant naso-
pharyngeal niche, leaving overall pneumococcal carriage
similar or only temporarily decreased (5,6) and lead to a
gradual increase in nonvaccine serotype disease (7). In ad-
dition, several studies have raised awareness of the replace-
ment of vaccine serotypes in the bacterial community with
other potential pathogens, such as Haemophilus influenzae
and Staphylococcus aureus in carriage or disease (8–11).
This replacement is likely explained by the highly interac-
tive nature of the microbiota in the natural habitat of the
specific bacterium (12).
The recent availability of high-throughput, deep-se-
quencing techniques has made it possible to obtain more
insight in the microbiota in humans, including the not yet
cultivated fraction of bacteria. These techniques have elu-
cidated that bacteria of the human microbiota outnumber
human host cells by 10-fold, and microbiota composition
varies greatly between body sites and persons. Coloniza-
tion is a dynamic process of interactions among microbes
Conjugate Vaccine and
in Healthy Children
Giske Biesbroek, Xinhui Wang,1 Bart J.F. Keijser,1 Rene M.J. Eijkemans, Krzysztof Trzciński,
Nynke Y. Rots, Reinier H. Veenhoven,2 Elisabeth A.M. Sanders, and Debby Bogaert
Keijser);? Julius? Center? for? Health? Sciences? and? Primary? Care,?
Utrecht? (R.M.J.? Eijkemans);? Netherlands? Vaccine? Institute,?
Bilthoven,? the? Netherlands? (N.Y.? Rots);? and? Spaarne? Hospital,?
1These authors contributed equally to this article.
and between microbes and the host and result in balanced
bacterial ecosystems that benefit health. Perturbations of
these interactive microbial structures (e.g., by environmen-
tal change or vaccinations) alter the bacterial network struc-
tures and may thereby influence the presence and contain-
ment of other microbiota members, and these alterations
have effects on health and susceptibility to disease (13,14).
Given the changes in pneumococcal serotypes, as well
as well as S. aureus and H. influenzae carriage after vac-
cination with PCV-7 (7,8), we questioned whether the ef-
fects of PCV-7 could be even more extensive than initially
believed. We therefore studied the effects of PCV-7 on the
complete nasopharyngeal microbiota of healthy children
in a randomized controlled trial by using deep-sequencing
techniques. The study was initiated shortly before nation-
wide implementation of PCV-7 in the Netherlands, there-
fore before herd effects appeared, which enabled us to mea-
sure the direct effects of the vaccine (15).
Study Design and Population
Nasopharyngeal samples were obtained from a ran-
domized controlled trial that studied efficacy of reduced-
dose schedules of PCV-7 on pneumococcal carriage in
1,005 healthy children in the Netherlands. The methods
of this trial have been described (15). In brief, participants
were randomly assigned to receive 1) PCV-7 at 2 and 4
months of age (2-dose group) of age; 2) PCV-7 at 2, 4, and
11 months of age (2 + 1-dose group); or 3) no PCV-7 (un-
vaccinated control group).
For the present study, we selected nasopharyngeal
samples of the group of children that received 3 vaccina-
tions with PCV-7 (n = 336) and of the group of children
that received no vaccinations with PCV-7 (controls) (n =
331). To avoid seasonal influences on microbiota compo-
sition (3), we selected samples from children whose first
birthday was during October 2006–January 2007. To avoid
interference from background DNA, only samples from
those children with sufficient bacterial density at 12 and 24
months of age (i.e., samples with DNA levels ≥1 pg/µL)
were selected for 454 pyrosequencing, as described (16).
Nasopharyngeal swab specimens from the controlled
trial had been obtained during home visits by using a deep
transnasal approach with a flexible, sterile, dry, cotton-
wool swab (TranswabPernasal Plain; Medical Wire and
Equipment Co., Ltd., Corsham, UK). Specimens were im-
mediately inoculated into transswab modified Amies Medi-
um, 483CE (Copan Diagnostics Inc., Murrieta, CA, USA),
transported to the laboratory, and stored in saline within
24 h at –80°C until further analyses. All nasopharyngeal
swab specimens were cultured for H. influenzae, Moraxella
catarrhalis, S. aureus, and Streptococcus pneumoniae and
subjected to pneumococcal serotyping (15,17,18). With
each nasopharyngeal swab specimen, a questionnaire on
risk factors for pneumococcal carriage in children and prior
antimicrobial drug use was completed.
The randomized controlled trial (NCT00189020) was
approved by an acknowledged Dutch National Ethics Com-
mittee (Stichting Therapeutische Evaluatie Geneesmiddel-
en) and conducted in accordance with European Statements
for Good Clinical Practice, which included the provisions
of the Declaration of Helsinki of 1989. Before enrollment,
written informed consent was obtained from both parents
of each participant.
Construction of Phylogenetic Library
The selected subset was processed for sequencing
of the 16S rDNA gene; the 454 GS-FLX-Titanium Se-
quencer (Life Sciences, Branford, CT, USA) was used for
sequencing. The 16SrDNA gene is a conserved gene with
variable regions among bacteria. Therefore, sequencing of
this gene enables detection of all bacteria in the microbi-
ota, which enables discrimination between bacterial taxa.
DNA was extracted and quantified by quantitative PCR
specific for conserved regions of the 16S rDNA gene. A
barcoded amplicon library was generated by amplifica-
tion of the V5–V7 hypervariable region of this gene and
sequenced unidirectional, which generated ≈1.5 million
sequences. Details of the methods have been described
(3,16) and are shown in the online Technical Appendix
pdf). The obtained sequences were processed and clas-
sified by using modules implemented in the Mothur
V.1.20.0 software platform (19–22). This platform en-
ables sequence classification on several taxonomic levels
on the basis of evolutionary relatedness. The smallest ac-
curate taxonomic level obtained by using 16S rDNA gene
sequencing is the operational taxonomic unit (OTU),
which is based on 97% similarity in nucleotide composi-
tion and enables differentiation just beyond genus level:
OTUs do not always discriminate between species, and
multiple OTUs might represent a specific genus, each
capturing distinct lineages within it.
For each of the samples, rarefaction curves were plot-
ted and sequence coverage was calculated by using the for-
mula 1 – (number of OTUs with a single sequence per sam-
ple/number of samples in the study) to ensure that sufficient
sequence numbers were analyzed. Sequence data were sub-
jected to weighted UniFrac analysis by using the UniFrac
module implemented in Mothur (23). The UniFrac metric
is a proxy for the distance between microbial communi-
ties based on evolutionary relatedness of lineages in each
sample. For all samples, we calculated the presence and
relative and absolute abundance of all OTUs. The relative
abundance was calculated as the proportion of sequences
assigned to a specific OTU divided by the overall number
of obtained sequences per sample. In addition, for the abso-
lute abundance, we multiplied the relative abundance of an
OTU by the obtained bacterial load per sample measured
by quantitative PCR.
Data analyses were performed by using R version 2.7
Excel 2011 (Microsoft, Redmond, WA, USA), and SPSS
version 15.0 (SPSS Inc., Armonk, NY, USA). We used
the Pearson χ2 test to compare baseline characteristics be-
tween PCV-7–vaccinated children and control children. To
visualize the weighted UniFrac dendrogram in relation to
metadata, we used iTOL version 2 software (24). We used
univariate and multivariate linear regression models (func-
tion Im and analysis of variance in software package R) to
study the effect of vaccination with PCV-7 on microbiota
profiles. We adjusted for antimicrobial drug use 1 month
before sampling, the presence of siblings, and daycare at-
tendance in all multivariate linear regression models. As-
sociations were considered statistically significant after
correction for multiple testing by determining the false-
discovery rate (q value 0.2). Relative effect sizes and their
95% CIs were calculated for all significant OTUs from
the standardized regression coefficients of the fitted linear
model, whereby 1 indicates no effect, >1 indicates higher
abundance, and <1 indicates less abundance in vaccinated
children than in controls.
Interindividual variability between vaccinated and
control children at 12 months and 24 months of age was
calculated by using Pearson correlations and tested for
significance by using the Mann-Whitney U test. We used
nonmetric multidimensional scaling (nMDS) to compare
microbiota profiles for dissimilarities and Euclidean dis-
tances to locate each sample in a low-dimensional space.
OTUs were clustered hierarchically by using average
linkage and Pearson correlation. The optimal number of
clusters was identified by using the Silhouette index. OTU
clusters and Pearson correlations between OTUs were dis-
played by using Cytoscape V2.8.2 (25).
Characteristics of Study Population and
We sequenced the nasopharyngeal microbiota of 97
children at 12 and 24 months of age who had received PCV-
7 at 2, 4, and 11 months of age, and 103 controls. Similar to
the main trial (15), in this subset of children, baseline char-
acteristics were not different between PCV-7 vaccinees and
controls (Table). Also, use of antimicrobial drugs was low,
especially in the month before sampling, and no correlation
was observed between antimicrobial drug use and vaccina-
tion with PCV-7 (partial correlation, r<–0.01).
Consistent with the main trial, vaccine serotype pneu-
mococcal carriage decreased in PCV-7–vaccinated chil-
dren. However, because of a lower number of children than
in main trial and loss of statistical power, we observed only
a trend toward increased carriage of nonvaccine-type pneu-
mococci (p = 0.08) at 24 months of age. Furthermore, the
increase in S. aureus carriage at 12 months of age in vac-
cinees observed in the main trial was not significant in this
subset because of a loss of power (Table) (18,26).
Symptoms of URTI
significant?difference?(p<0.05).?PCV-7,?7-valent pneumococcal conjugate vaccine; NS, not significant (p>0.1);?URTI, upper respiratory tract infection.
†Defined as at least 4 h/wk of daycare with >1 child from a different family.
‡Presence of mild symptoms of a respiratory tract infection at time of sampling as reported by parents.
PCV-7,?n?=?97 Control,?n?=?103 p value
Sequence and Microbiota Characteristics
We obtained 1,016,934 high-quality sequences (mean
± SD 2,561 ± 767 sequences/sample). Sequence depth was
sufficient to obtain a high degree of sequence coverage for
all samples (mean 0.995, median 0.996, range 0.975–1).
Sequencing of nasopharyngeal microbiota identified a di-
verse ecosystem dominated by the well-known bacterial
genera Moraxella, Streptococcus, and Haemophilus, but
also Dolosigranulum and Corynebacterium (online Tech-
nical Appendix Table 1). In addition, we detected a range
of lower abundant bacterial genera (424 OTUs excluding
singletons), present in either many (Escherichia/Shigella,
Neisseria, and Gemella spp.) or few (Sneathia and Porphy-
romonas spp.) children. We found that for most children,
the microbiota profile was determined mostly by abun-
dance of the 5 predominant OTUs, and did not differ in
children at 12 and 24 months of age (Figure 1).
To discriminate potential pathogens in the OTU set, we
correlated the culture results of the samples with the corre-
sponding OTUs of Moraxella, Streptococcus, Haemophi-
lus, and Staphylococcus. We observed a strong correlation
between culture results and the highest ranking OTUs for
the respective genera (p<0.005) (online Technical Appendix
Table 2), which indicated a strong representation of these
potential pathogens within these OTUs.
Nasopharyngeal Microbiota Composition in Vaccinees
To evaluate the effect of vaccination with PCV-7 on
the overall microbial community composition, we first cal-
culated the degree of dissimilarity in microbiota composi-
tion between vaccinees and controls by using nMDS (27).
We observed a significant shift in microbiota profiles be-
tween vaccinated and nonvaccinated children at 12 months
of age (geometric means; p = 0.01, by F-test) but not at 24
months of age (Figure 2).
Because nMDS suggested higher variability of com-
munity profiles in vaccinees, we calculated interindividu-
al variability in microbiota composition among vaccinees
and controls by using Pearson correlations. We con-
firmed higher interindividual variability (i.e., less simi-
larities between profiles) among vaccinees than in control
children at 12 months of age (median correlation coef-
ficient r = 0.39 vs. 0.41, p<0.0001) than at 24 months of
age (median correlation coefficient r = 0.42 vs. 0.44, p
= 0.006). At 12 months of age, this variability was ac-
companied by a significantly higher number of OTUs per
community profile (i.e., higher diversity of bacteria) in
vaccinated children (median 20, range 6–82) than in un-
vaccinated controls (median 17, range 4–46; p = 0.002)
(online Technical Appendix Table 3).
In univariate and multivariate linear regression mod-
els, these changes in overall community composition,
variability, and bacterial diversity in vaccinated children
were accompanied by significant (false-discovery rate q
value <0.2, p<0.0003) increases in relative and absolute
abundance of anaerobic bacteria (e.g., Veillonella spp.,
relative effect size [RES] 3.90, 95% CI 2.13–7.17; Pre-
votella spp., RES 7.24, 95% CI 4.06–12.94; unclassified
Bacteroidetes spp., RES 2.41, 95% CI 1.28–4.54; and
Leptotrichia spp., RES 3.31, 95% CI 1.78–6.16) as well
as increases in relative and absolute abundance of several
streptococcal OTUs (RES 4.53, 95% CI 2.48–8.30). A
trend (0.005<p< 0.05) toward higher abundance of gram-
positive Actinomyces spp. (RES 3.00, 95% CI 1.60–5.62)
and Rothia spp. (RES 2.43, 95% CI 1.29–4.58), the gram-
negative Neisseria spp. (RES 2.12, 95% CI 1.13–3.99),
and the anaerobes Fusobacterium spp. (RES 1.93, 95%
CI 1.02–3.64) and Megasphaera spp. (RES 1.96, 95%
CI 1.03–3.71) was also observed after vaccination with
PCV-7. In addition, we found apparent higher absolute
abundance of Haemophilus (RES 1.33, 95% CI 0.73–
2.44) and Staphylococcus (RES 1.56, 95% CI 0.83–2.93)
species in vaccinated children at age 12 months (Figure
3). At 24 months of age, differences between vaccinees
and controls had largely disappeared.
Although antimicrobial drug use was low, we observed
a trend (0.01<p< 0.05) toward decreased relative abun-
dance of Dolosigranulum (RES 0.28, 95% CI 0.061–1.33)
and Corynebacterium (RES 0.28, 95% CI 0.061–1.30) and
increased abundance of Staphylococcus (RES 6.29, 95% CI
1.38–28.77) in children who received antimicrobial drugs
in the month before sampling.
Microbial Inference Network in Controls and Vaccinees
Because microbial ecosystems form interacting net-
works of microorganisms, the presence (or abundance) of
1 type of bacteria will most likely affect the presence of
others. To obtain better insight into the effect of vaccina-
tion on the bacterial community structure, we evaluated
the effect of vaccination with PCV-7 on the microbial
interaction network by using network inference analysis
(Figure 4). OTUs were hierarchically clustered and dis-
played with their Pearson correlation by using Cytoscape
V2.8.2 for control (Figure 4, panel A) and vaccinated
(Figure 4, panel B) children. At the age of 12 months,
children showed clear shifts in cluster distribution, com-
position, and interrelatedness after vaccination with
PCV-7. In general, as a consequence of vaccination with
PCV-7, several independent clusters observed in controls
merged into 1 large cluster in vaccinees: this cluster in-
cluded gram-negative anaerobes (Prevotella, Veillonella,
and Fusobacterium spp.) as well as Actinomyces and
Neisseria spp. and several streptococcal species. Bacte-
ria that had expanded as a consequence of vaccination all
belonged to the merged cluster or a single distinct cluster
containing mostly Prevotella, unclassified Bacteroidetes,
Fusobacterium, Streptococcus, and Neisseria spp. (clus-
ter 8). The cluster containing the predominating poten-
tial pathogens Staphylococcus and Haemophilus spp. in
controls (cluster 1) was divided in vaccinees because of
changed behavior, in particular that of the Staphylococcus
The novelty of the present study was use of deep-se-
quencing analyses. By using these analyses, we gained a
far broader insight into the effect of PCV-7 on bacterial
carriage at the ecologic niche of pneumococci without re-
stricting selection to cultivable or well-known potential
pathogens. We showed that vaccination with PCV-7 has
a marked effect on the complete microbiota composition
of the upper respiratory tract in children. This effect goes
far beyond the shifts in pneumococcal serotypes distribu-
tion (7,15) and well-known potential pathogens reported
(8). Vaccination with PCV-7 resulted in a shift in bacte-
rial community composition and structure, with an increase
in presence or abundance of several anaerobes, such as
Veillonella, Prevotella, Fusobacterium, and Leptotrichia
species; gram-positive bacteria, such as Actinomyces and
Rothia species, and nonpneumococcal streptococci; and
gram-negative Neisseria species.
Shifts in newly acquired or expanded OTUs concern
mainly commensal organisms that are in general more
predominantly present in the oropharynx than in the naso-
pharynx (28,29). Because the reduction in carriage of the
7 specific pneumococcal serotypes after PCV-7 adminis-
tration correlated highly with emergence and expansion
of these oropharyngeal types of species, this finding might
suggest that after eradication of a common colonizer, such
as vaccine serotype pneumococci, momentum is created
for species from surrounding regions to colonize or ex-
pand in the vacant nasopharyngeal niche. In support of
this hypothesis, Tano et al. (30) reported negative asso-
ciations between S. pneumoniae, particularly PCV-7 se-
rotypes, and other streptococcal species in healthy young
children. Moreover, Laufer et al. (31) reported negative
associations between S. pneumoniae and the presence of
(23) of nasopharyngeal samples
of? children? at? 12? and? 24? months?
of? age? vaccinated? with? 7-valent?
pneumococcal conjugate vaccine.
Clustering? of? samples? was? based?
relatedness by using Weighted
UniFrac? analyses.? Clustering? is?
shown in a circle dendrogram.
Each branch represents a sample
and each adjacent
represents the relative abundance
of the top 5 operational taxonomic
units (OTUs) found in that sample.
Differences in length of branches
each other. Branches of reference
samples were collapsed and are
represented? by? black? triangles.?
Samples are mostly dominated
and Haemophilus spp., or the
and Corynebacterium spp., which
highly affects sample clustering
by? Weighted? UniFrac.? Branches?
are colored according to age of
sampled? children? (purple? =? 12?
months,? green? =? 24? months).? No?
clear clustering of samples by age
Veillonella, Neisseria, Rothia, and Actinomyces spp. in
nasal swab specimens from children with upper respira-
tory tract symptoms, a finding that is consistent with the
influx pattern of bacteria we observed after vaccination
In addition to this shift in microbiota profiles, we also
observed increased bacterial diversity and interindividual
variability after vaccination with PCV-7. This influx or
outgrowth of anaerobes and other bacteria might lead to
a disequilibrium with the host. These species might be at
a disadvantage again when nonvaccine serotypes fill in
the gap, which would lead to a restored host-microbiome
equilibrium.This hypothesis could explain why we ob-
served the strongest PCV-7 effect on microbiota in chil-
dren at 12 months of age (1 month after administration
of the last PCV-7 dose) and not at 24 months, because
serotype replacement has already become apparent at this
The mechanisms and consequences of this change in
community composition and structure after vaccination
with PCV-7 remain mostly speculative. In general, tempo-
rary disequilibria of bacterial composition (dysbiosis) are
associated with an increased risk for disease, as has been
shown for the gut (14) and oral niches (32). Moreover, the
combination of some of the emerging bacteria (Veillonella,
Actinomyces, Rothia, and Neisseria spp.) are associated
with increased risk for otitis media (31). Nevertheless, in
our study, we did not obtain samples during respiratory
tract infections and were therefore unable to link observed
changes in microbiota structure with susceptibility to respi-
ratory tract infections. Therefore, short-term and long-term
surveillance during health and disease seems warranted to
understand the full implications of vaccine-induced chang-
es in microbiota structure.
Although increased presence or abundance of S.
aureus and H. influenzae at 12 months of age was not
significant in this subset of children, we observed an in-
crease in culture-proven S. aureus carriage in the origi-
nal randomized controlled trial (18), as well as further
increases in culture-proven S. aureus and H. influenzae
carriage observed in surveillance studies 3–5 years after
PCV-7 implementation in the Netherlands (8). These find-
ings are consistent with negative associations between S.
pneumoniae (particularly PCV-7 serotypes) and S. aureus
(33,34) and H. influenzae (35–37) observed in healthy
nonimmunized children. Nontypeable H. influenzae and
of? children? vaccinated? with? 7-valent?
and? control? children? at? 12? and? 24?
months? of? age.? Microbiota? profiles?
were compared between groups by
using? nMDS? to? find? dissimilarities?
between samples and locate samples
represents? the? microbiota? profile? of?
a sample. Boxes indicate geometric
means of both groups in which the
length of the line between the sample
(circle) and the geometric mean (box)
indicates the distance of that sample
indicate higher distances of samples
(i.e., higher variability between sample
compositions). A) nMDS plots of
vaccinated children (blue lines) and
controls? (red? lines)? at? 12? months? of?
age. The geometric mean of microbiota
profiles? differed? significantly? (p? =?
0.01,? by? F-test)? between? vaccinated?
children and controls. B) nMDS plots
of vaccinated children (blue lines)
of age, showing no differences in
S. aureus were also more frequently isolated from persons
with acute otitis media after introduction of PCV-7 in na-
tional immunization programs (38–40), which indicates
that carriage may reflect disease dynamics. Together with
S. pneumoniae nonvaccine serotype replacement, these
effects may further jeopardize the net health benefit of
vaccinations with PCV.
Some limitations of our study should be recognized.
First, this study was limited to a representative subset of the
original study of 1,003 infants. Second, to avoid seasonal
bias (3) in microbiota composition, we analyzed samples
from only the winter season. Third, children who received
antimicrobial drugs before sampling were not excluded
from the analyses because only a small number of children
received these drugs and we observed no correlation be-
tween antimicrobial drug use and vaccination with PCV.
Furthermore, the observed associations between antimicro-
bial drug use and microbiota composition were also differ-
ent from the vaccination effect of PCV-7.
One strength of this study was the randomized con-
trolled study design, which enabled us to attribute changes
in microbiota profiles directly to the conjugate vaccine in-
dependent of secular trends or other external confounders.
Furthermore, recruitment in this study was completed well
before implementation of PCV-7 in the Dutch vaccina-
tion program for newborns, and vaccine-induced changes
in this randomized controlled trial setting might therefore
become more apparent in the open population several years
after introduction due to herd effects (5,7)
Our study indicates that vaccination against a common
colonizer affects microbiota composition and structure.
This finding underlines the need for more detailed under-
standing of microbiota dynamics and interactions between
its inhabitants. Overall, because infants might be vulner-
able to community disruptions and dysbiosis, we recom-
mend that new trials, such as studies on efficacy of broader
pneumococcal coverage vaccines, consider the effect of
vaccination on the commensal flora in its totality instead of
only on a single species.
We thank Elske J.M. van Gils, Gerwin D. Rodenburg, and
the research team for conducting the randomized controlled trial;
Jacob Bruin for organizing and supervising laboratory logistics;
study and laboratory staff and collaborating institutes for their
dedication to this project; and the children and their families for
participating in this study.
This study was supported by the Netherlands Organiza-
tion for Scientific Research (NWO-VENI grant 91610121 and
ZonMw grant 91209010). The randomized controlled trial (Clini-
calTrials.gov NCT00189020) was supported by the Dutch Minis-
try of Health.
Ms Biesbroek is an MD and PhD candidate at the Wilhelmi-
na Children’s Hospital, University Medical Center, Utrecht, the
Netherlands. Her research interests include molecular character-
ization and epidemiology of the microbiota in the respiratory tract
(OTUs) in children vaccinated with
7-valent? pneumococcal? conjugate?
vaccine? and? control? children? at? 12?
abundant OTUs are represented by
in vaccinated children than in
controls? (p<0.0003).? Although? not?
average absolute abundance was
observed for Haemophilus and
Staphylococcus spp. in vaccinated
months of age. †OTUs that showed
a trend toward higher abundance in
vaccinated children than in controls
vaccinated or controls by using a log2?scaling.?OTUs?that?were?significantly?higher?in?vaccinated?children?are?indicated?by?red?circles?around?
(controls),?we?identified?13?OTU?clusters.?Haemophilus influennzae and Staphylococcus aureus clustered together in a small cluster distant
from?the?other?OTUs?(cluster?1).?Streptococcus pneumoniae formed,?together?with?2?other?OTUs,?a?separate?cluster?that?was?also?distant?from?
distribution between vaccinated and unvaccinated children were also observed. Staphylococcus aureus drifted?from?cluster?1?in?controls?
present in that cluster and because of emergence of new OTUs within the cluster. In addition, after vaccination, cluster 3 including Moraxella
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Address for correspondence: Debby Bogaert, Department of Pediatric
Immunology and Infectious Diseases, Wilhelmina Children’s Hospital,
University Medical Center Utrecht, PO Box 85090, Rm KC.03.068.0,
3584 EA Utrecht, the Netherlands; email: firstname.lastname@example.org