High Nasopharyngeal Carriage of Non-Vaccine Serotypes
in Western Australian Aboriginal People Following 10
Years of Pneumococcal Conjugate Vaccination
Deirdre A. Collins1*☯, Anke Hoskins1☯, Jacinta Bowman2, Jade Jones2, Natalie A. Stemberger2,3, Peter C.
Richmond4, Amanda J. Leach5, Deborah Lehmann1
1 Telethon Institute for Child Health Research, Centre for Child Health Research, the University of Western Australia, Perth, Western Australia, Australia,
2 Division of Microbiology & Infectious Diseases, PathWest Laboratory Medicine WA, Perth, Western Australia, Australia, 3 Microbiology & Immunology, School
of Pathology and Laboratory Medicine, the University of Western Australia, Perth, Western Australia, Australia, 4 School of Paediatrics and Child Health,
University of Western Australia, Perth, Western Australia, Australia, 5 Menzies School of Health Research, Charles Darwin University, Darwin, Northern
Background: Invasive pneumococcal disease (IPD) continues to occur at high rates among Australian Aboriginal
people. The seven-valent pneumococcal conjugate vaccine (7vPCV) was given in a 2-4-6-month schedule from
2001, with a 23-valent pneumococcal polysaccharide vaccine (23vPPV) booster at 18 months, and replaced with
13vPCV in July 2011. Since carriage surveillance can supplement IPD surveillance, we have monitored
pneumococcal carriage in western Australia (WA) since 2008 to assess the impact of the 10-year 7vPCV program.
Methods: We collected 1,500 nasopharyngeal specimens from Aboriginal people living in varied regions of WA from
August 2008 until June 2011. Specimens were cultured on selective media. Pneumococcal isolates were serotyped
by the quellung reaction.
Results: Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis were carried by 71.9%,
63.2% and 63.3% respectively of children <5 years of age, and 34.6%, 22.4% and 27.2% of people ≥5 years. Of 43
pneumococcal serotypes identified, the most common were 19A, 16F and 6C in children <5 years, and 15B, 34 and
22F in older people. 7vPCV serotypes accounted for 14.5% of all serotypeable isolates, 13vPCV for 32.4% and
23vPPV for 49.9%, with little variation across all age groups. Serotypes 1 and 12F were rarely identified, despite
causing recent IPD outbreaks in WA. Complete penicillin resistance (MIC ≥2µg/ml) was found in 1.6% of serotype
19A (5.2%), 19F (4.9%) and 16F (3.2%) isolates and reduced penicillin susceptibility (MIC ≥0.125µg/ml) in 24.9% of
isolates, particularly 19F (92.7%), 19A (41.3%), 16F (29.0%). Multi-resistance to cotrimoxazole, tetracycline and
erythromycin was found in 83.0% of 23F isolates. Among non-serotypeable isolates 76.0% had reduced susceptibility
and 4.0% showed complete resistance to penicillin.
Conclusions: Ten years after introduction of 7vPCV for Aboriginal Australian children, 7vPCV serotypes account for
a small proportion of carried pneumococci. A large proportion of circulating serotypes are not covered by any
currently licensed vaccine.
Citation: Collins DA, Hoskins A, Bowman J, Jones J, Stemberger NA, et al. (2013) High Nasopharyngeal Carriage of Non-Vaccine Serotypes in Western
Australian Aboriginal People Following 10 Years of Pneumococcal Conjugate Vaccination. PLoS ONE 8(12): e82280. doi:10.1371/journal.pone.0082280
Editor: Eliane Namie Miyaji, Instituto Butantan, Brazil
Received June 18, 2013; Accepted October 22, 2013; Published December 3, 2013
Copyright: © 2013 Collins et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Funding for this study was provided by Western Australia Department of Health through the Collaboration for Applied Research and Evaluation
and National Health and Medical Research Council Project Grant #545232. The funders had no role in study design, data collection and analysis, decision
to publish, or preparation of the manuscript.
Competing interests: AH and AL have received research funding and support to attend conferences from GlaxoSmithKline and Pfizer Australia. PR has
been a member of vaccine advisory boards for Wyeth and CSL Ltd and has received institutional funding for investigator-initiated research from
GlaxoSmithKline Biologicals and Merck and received travel support from Pfizer and Baxter to present study data at international meetings. DL has been a
member of the GlaxoSmithKline Australia Pneumococcal-Haemophilus influenzae-Protein D conjugate vaccine (‘‘Phid-CV’’) Advisory Panel, has received
support from Pfizer Australia and GlaxoSmithKline Australia to attend conferences, has received an honorarium from Merck Vaccines to give a seminar at
their offices in Pennsylvania and to attend a conference, and is an investigator on an investigator-initiated research grant funded by Pfizer Australia. This
does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. All other authors have indicated they have no conflicts of
* E-mail: email@example.com
☯ These authors contributed equally to this work.
PLOS ONE | www.plosone.org1December 2013 | Volume 8 | Issue 12 | e82280
Invasive pneumococcal disease (IPD), which includes
pneumonia, meningitis, and septicaemia, causes an estimated
476,000 deaths in children < 5 years annually, the majority of
which occur in the third world . In Western Australia (WA)
between 1997 and 2007, the overall IPD incidence rate was 47
cases per 100,000 population per year in Aboriginal people, 6.7
times higher than the IPD incidence in non-Aboriginal people
. Furthermore, Aboriginal children experience high rates of
otitis media (OM), often caused by Streptococcus pneumoniae,
with up to 21% of children in WA having a tympanic membrane
perforation before the age of 2 years in remote areas . OM
and its complications can have profound effects on hearing and
subsequently can impact
development and behaviour. Overcrowding and indoor smoking
are common in the Aboriginal population and associated with
increased risk of nasopharyngeal bacterial carriage which is a
necessary precursor to IPD and OM .
In 2001 the seven-valent pneumococcal conjugate vaccine
(7vPCV, Prevenar®), covering serotypes 4, 6B, 9V, 14, 18C,
19F and 23F, was introduced for Aboriginal Australian children
in a 2-4-6-month schedule, with a catch-up schedule for
children < 2 years of age, and for children < 5 years of age with
predisposing medical conditions. A booster of 23-valent
pneumococcal polysaccharide vaccine (23vPPV, Pneumovax
23®, covers 7vPCV serotypes and 1, 2, 3, 5, 7F, 8, 9N, 10A,
11A, 12F, 15B, 17F, 19A, 20, 22F and 23F) was offered at age
18 months to Aboriginal children. In 2005 the 7vPCV program
was extended to include all Australian children. On 1 July 2011
13vPCV replaced 7vPCV (covering six additional serotypes; 1,
3, 5, 6A, 7F, 19A) in the immunization schedule and a fourth
dose of 13vPCV replaced the 23vPPV booster in Aboriginal
children. Since the introduction of 7vPCV, the incidence of IPD
caused by vaccine serotypes has fallen but IPD due to
non-7vPCV serotypes has increased, and almost doubled in
WA Aboriginal adults aged 30-49 years . Serotypes which
have emerged since the introduction of 7vPCV in WA include
1, 12F and 19A .
Surveillance of IPD in WA is limited by the need to
administer antibiotics in remote areas before a sample of blood
for culture can be collected at a referral hospital, and by the low
sensitivity of blood culture. In addition, the Aboriginal
population in WA is relatively small (around 77,000), and while
the incidence of IPD is high, small numbers of cases make it
difficult to monitor trends effectively. Given these limitations,
surveillance of nasopharyngeal pneumococcal carriage assists
in identifying serotypes circulating in the population, helping to
predict changes in serotypes causing IPD . Carriage studies
facilitate monitoring the impact of PCV programs, which alter
carriage and associated
pneumococcal carriage also allows antimicrobial susceptibility
patterns to be monitored which can guide management of
common non-invasive infections such as OM and pneumonia.
While few reports exist on pneumococcal carriage in
Aboriginal Australians prior to the introduction of 7vPCV,
carriage studies in the Northern Territory indicate that 7vPCV
on speech and language
herd immunity. Studying
reduced carriage of 7vPCV serotypes, similar to trends
observed elsewhere [7–9].
Since 2008, we have studied nasopharyngeal carriage of
bacterial pathogens in the Aboriginal population in WA. Our
aim is to monitor nasopharyngeal carriage of pneumococcal
serotypes, as well as the prevalence of other commonly carried
pathogens, namely Haemophilus
catarrhalis and Staphylococcus aureus, in Aboriginal children
and adults living in Western Australia. Here we report on
carriage rates of bacteria, and serotype distribution and
antimicrobial susceptibility of pneumococci in children and
adults in WA until the introduction of 13vPCV.
WA covers an area of 2.5 million km2, with a range of
climates from tropical northern Kimberley to the warm
temperate southwest coast, to the inland desert. There is a
sparse population of 2.2 million people (population density 0.9
persons/km2) (Figure 1). Aboriginal people make up 3% of the
population. Approximately two-thirds live in non-metropolitan
regions, in communities ranging from small and very remote
(e.g. Laverton; Aboriginal population 339 among 1,227 in total)
to regional towns (e.g. Kalgoorlie; 889 among 13,949 total)
. In the Perth metropolitan region, Aboriginal people
numbered 12,852 among 1.7 million in the 2011 Census .
Procedures. From August 2008 until June 2011, we visited
communities with Aboriginal populations across WA for data
collection. Study participants attending health services for
routine examination, immunization or illness who identified as
Aboriginal were recruited opportunistically. People were also
recruited during home visits. Non-Aboriginal people were
excluded, as were those with severe congenital abnormalities.
After obtaining informed written consent, demographic and
environmental data were collected including smoking behaviour
of family members and the number of people sharing a home.
We recorded information about past and present health status
and recent antibiotic use. Where possible, medical records
were examined to obtain further details on recently prescribed
antibiotics and illness. The Australian Childhood Immunisation
Register (ACIR) was later consulted to record the vaccination
status of children born from 1998 onwards. ACIR records were
accessed using participants’ names and dates of birth. Children
were classified as “vaccinated” with 7vPCV if they had received
at least two doses of 7vPCV at least 2 weeks prior to specimen
Nasopharyngeal swabs (NPS) were collected using a nylon
flocked swab (Copan Diagnostics Inc., USA). If participants
were reluctant to provide a NPS, a nose-blown sample on a
clean tissue was swabbed . Swabs were stored in 1 mL
skim milk-tryptone-glucose-glycerol broth in a portable cooler
until transfer to a liquid nitrogen dry shipper at ≤ -80°C within
12 hours for transport by road or air to PathWest Laboratory
Medicine WA in Perth, where they were stored at -80°C.
Pneumococcal Carriage in Australian Aboriginals
PLOS ONE | www.plosone.org2December 2013 | Volume 8 | Issue 12 | e82280
Microbiological methods. Primary culture was carried out
as described previously . Briefly, swabs were cultured on
selective media for common nasopharyngeal bacteria.
Subcultured isolates were confirmed as S. pneumoniae by
optochin susceptibility, and H. influenzae, M. catarrhalis and S.
aureus were confirmed by standard criteria . Two
pneumococcal isolates (or more, if morphologically distinct) per
positive culture were stored and serotyped by the Quellung
reaction using antisera obtained from the Statens Serum
Institut, Denmark. Serotypes were validated at Menzies School
of Health Research, Darwin, if an inconclusive Quellung result
was obtained. Isolates that could not be serotyped by Quellung
are referred to as “non-serotypeable”. Susceptibility to
penicillin, ceftriaxone, cotrimoxazole,
chloramphenicol and tetracycline was determined using the
disc diffusion method. Minimum inhibitory concentrations
(MICs) to penicillin and ceftriaxone in isolates showing reduced
susceptibility by disc diffusion were determined by E-test
(bioMérieux Diagnostics, France). Antibiotic resistance was
classified according to the Clinical and Laboratory Standards
Institute guidelines .
Analysis. Since a minimum of two isolates were serotyped
for each sample, results were aggregated according to
serotype to calculate the proportion of individual serotypes
among all isolates. Descriptive analyses were performed using
SPSS 15.0 for Windows. Proportions were compared between
different groups using the χ2 test.
Ethics approval and community consultation
Ethical approval to conduct this study was granted by the
Princess Margaret Hospital for Children Ethics Committee, the
Western Australian Country Health Service Board Research
Ethics Committee and the Western Australian Aboriginal Health
Ethics Committee. Approval to approach communities in the
Kimberley was also granted by the Kimberley Aboriginal Health
Planning Forum. Prior to planning a visit, we consulted local
Aboriginal community committees and/or councils to inform
them of our study and seek approval to visit at an appropriate
time. Written informed consent was obtained from next of kin,
caretakers or guardians on behalf of children participants
involved in the study, and adults provided written consent for
their own participation.
We visited 40 communities across WA in the following
regions: the Kimberley, Goldfields, Pilbara, Gascoyne, as well
as the metropolitan area of Perth and its surroundings (Figure
1). From August 2008 to June 2011, 1,473 NPS and 27 nose-
blown samples were collected and 1,430 questionnaires were
completed. Participants ranged in age from < 24 hours to 101
years. While 44.9% of all participants were male, among adults
there were more female than male participants (Table 1). The
number of participants aged < 5 years or ≥ 5 years by region is
shown in Figure 1. At the time of specimen collection, 179/1430
(12.5%) people reported they were sick, 107 (7.5%) reported
respiratory symptoms. Eight hundred and seven (56.4%) lived
in a home where at least one person smoked inside, and 880
(61.5%) lived in a home with at least six inhabitants. Sixty-eight
(4.8%) reported taking antibiotics in the previous 4 weeks, 17
of whom were still taking them at the time of swab collection.
Of 861 children born from 1998 onwards, 486 (56.4%) could be
identified on ACIR, and 464 (95.4%) of these had received at
least two doses of 7vPCV prior to specimen collection.
Carriage rates by age group
S. pneumoniae, H. influenzae and M. catarrhalis were
carried by 71.9%, 63.2% and 63.3% respectively of children < 5
years of age, and 34.6%, 22.4% and 27.2% of people ≥ 5
years. Pneumococcal carriage rates were 74.1% in females
and 70.0% in males < 5 years, and 30.6% in females and
40.9% in males ≥ 5 years. More detailed age-specific bacterial
carriage rates are shown in Table 1. Among infants aged < 6
months, 49.3% carried S. pneumoniae. The highest rate of
pneumococcal carriage was in children aged 6-11 months
(Table 1). Of particular note, 33.3% of infants < 2 months of
age, who were not yet eligible for their first dose of 7vPCV,
carried S. pneumoniae (not shown). We found no significant
difference in pneumococcal carriage in people reporting
Table 1. Number of swabs collected, proportion collected from male participants (%) by age group and age-specific
prevalence (%) of S. pneumoniae, H. influenzae, M. catarrhalis and S. aureus carriage.
Age Number of swabsMale S. pneumoniae H. influenzae M. catarrhalis S. pneumoniae, H. influenzae and M. catarrhalis S. aureus
< 6 mth7353.4 49.3 41.147.9 17.830.1
6-11 mth6159.0 85.265.660.634.5 11.5
12-23 mth12661.176.971.4 66.749.07.1
2-4 yr30251.372.564.6 184.108.40.206
5-14 yr47652.349.435.741.218.0 16.1
15-29 yr 21822.520.6 9.011.0 3.213.8
30-49 yr 17126.920.510.5220.127.116.11
≥ 65 yr 21 42.9 19.04.7 28.6014.3
Pneumococcal Carriage in Australian Aboriginals
PLOS ONE | www.plosone.org3December 2013 | Volume 8 | Issue 12 | e82280
respiratory symptoms compared to those who were not
(p = 0.24).
Region-specific S. pneumoniae carriage rates for participants
< 5 and ≥ 5 years are shown in Figure 1. No swabs were
collected in the Wheatbelt and Great Southern regions of WA.
In children < 5 years carriage rates ranged from 50.0% in the
South West-Peel region to 76.6% in the Midwest-Murchison
region; in older people carriage rates were highest in the
Midwest-Murchison region (41.6%) and lowest in the Perth
Metro area (27.3%, Figure 1).
Simultaneous carriage of S. pneumoniae, H. influenzae and
M. catarrhalis was observed in 40.9 % of children < 5 years.
Among adults, M. catarrhalis was most commonly carried in
those aged ≥ 50 years, while H. influenzae was rarely carried in
Figure 1. Prevalence of S. pneumoniae carriage in 1500 Aboriginal people (<5 years, ≥ 5 years) by Western Australian
health regions. N = number of nasopharyngeal swabs collected per region for participants (< 5 years, ≥ 5 years). Overall, the
prevalence of S. pneumoniae carriage was 71.9% in children < 5 years, and 34.6% in people ≥ 5 years. Specimens were collected 1
Aug 2008 - 30 June 2011.
Pneumococcal Carriage in Australian Aboriginals
PLOS ONE | www.plosone.org4 December 2013 | Volume 8 | Issue 12 | e82280
adults ≥ 50 years (Table 1). The carriage rate of S. aureus was
12.6%, the highest rate being in children aged < 6 months
(30.1%, Table 1). Other bacteria that were carried less
frequently included Lancefield Group A streptococci (1.6%
overall) and Lancefield Group C streptococci (0.9%).
Among 729 pneumococcus-positive cultures we identified
856 distinct isolates, of which 730 were typed to 43 different
serotypes, and 126 (14.7%) were non-serotypeable (Table 2).
The age-specific distribution of the 12 most common serotypes
is shown in Figure 2. For children < 2 years, the most common
carriage serotypes were 19A, 16F, 6C, and 19F. In children
aged 2-14 years, the most common serotypes were 6C, 23F,
19A and 16F. The most common serotypes in adults were 15B,
34 and 6C. Overall, 114 (15.6%) pneumococcus carriers of all
ages had two strains identified, while six carriers had three
strains identified. One strain was nonserotypeable in 55
(45.8%) cases of multiple strain carriage and the most common
serotype was 16F in 17 (13.8%) cases.
Proportion of pneumococcal carriage serotypes
covered by different vaccine formulations
Overall, we found 14.5% of serotypeable pneumococci were
7vPCV serotypes, equivalent to a prevalence of 7.0%. 13vPCV
(which covers four of the 12 most common serotypes found in
this study, namely 6A, 19A, 19F and 23F, but not 6C) would
have covered 32.4% of serotypes carried during the study
period across all ages. Half (50.1%) of the serotypes found are
not included in any currently licensed vaccine (Figure 3). The
proportion of serotypes covered by each of the three vaccines
varied little with age, although a higher proportion of
pneumococci were non-vaccine serotypes in adults than in
younger people (Figure 3).
Resistance to cotrimoxazole was present in 263 (30.6%) of
all 857 pneumococcal isolates, while 156 (18.2%), 82 (9.5%),
14 (1.6%), one (0.001%) and one (0.001%) isolates were
resistant to erythromycin, tetracycline, penicillin (MIC ≥ 2µg/ml),
chloramphenicol and ceftriaxone (MIC ≥ 2µg/ml), respectively
(Table 2). Reduced susceptibility to penicillin (MIC ≥
0.125µg/ml) was present in 227 (26.5%) isolates. Of the 58
serotype 19A isolates, 28 (48.3%) were resistant to
cotrimoxazole and 27 (46.6%) had reduced susceptibility to
penicillin; 38 (97.6%) of 41 19F isolates had reduced penicillin
susceptibility. Complete penicillin resistance (MIC ≥ 2µg/ml)
was identified in nine isolates (1.2%): three (5.2%) serotype
19A, two (4.7%) 19F and one (7.1%) 22A isolate.
Chloramphenicol resistance was found in a single isolate of
serotype 15C. Multi-resistance to tetracycline, cotrimoxazole
and erythromycin was observed in 36 (83.7%) serotype 23F
isolates, and seven (5.5%) non-serotypeable isolates. Of 126
non-serotypeable isolates, 59 (46.9%) were resistant to
cotrimoxazole and 101 (80.2%) had reduced penicillin
susceptibility, five of which were completely resistant to
Figure 2. Distribution of the 12 most common pneumococcal serotypes by age group.
Pneumococcal Carriage in Australian Aboriginals
PLOS ONE | www.plosone.org5December 2013 | Volume 8 | Issue 12 | e82280
This is the first assessment of pneumococcal carriage in
Aboriginal people in WA in the PCV era. The PCV program
aimed to reduce the burden of invasive pneumococcal disease
(IPD) but we also anticipated that it would alter the serotypes
that are carried in the nasopharynx. While pneumococcal
carriage rates were high, 7vPCV serotypes were rarely carried.
Despite a lack of data on carriage serotypes in WA prior to
introduction of 7vPCV, it is likely that the vaccination program
Table 2. Frequencies of serotypes and antibiotic resistance rates found among 856 isolates of S. pneumoniae.
Serotype Number of isolatescotrR (%) eryR (%) tetR (%) penI (%) penR (%)
6A37 8.1 62.10 2.70
6C 7373.9 4.1000
9N8 12.587.587.5 00
11A 3915.900 5.10
19F41 2.40092.7 4.9
22A14 14.3000 7.1
22F21 071.4 000
23F4390.7 90.7 86.04.7 2.3
33D20 100.00 100.00
NT12646.9 27.0 9.576.24.0
TOTAL 85630.7 18.2 9.5 24.9 1.6
43 serotypes were identified among 730 serotypeable isolates, 126 isolates were non-serotypeable (NT). cotr: cotrimoxazole, ery: erythromycin, tet: tetracycline, pen:
penicillin, R: resistant, I: intermediate resistance
Pneumococcal Carriage in Australian Aboriginals
PLOS ONE | www.plosone.org6December 2013 | Volume 8 | Issue 12 | e82280
has contributed to reducing carriage of 7vPCV serotypes. IPD
due to 7vPCV serotypes accounted for 40% of IPD in
1997-2001 compared with 12% in 2005-2007 . The high
carriage rates of non-7vPCV serotypes may counterbalance
the benefits of the vaccine, assuming that some non-7vPCV
serotypes may display similar or higher disease potential .
The high pneumococcal carriage rates found in this study
correspond well with studies in the Northern Territory of
Australia where prevalence of carriage surpassed 80% in
children aged 2-4 years in a cross-sectional study carried out in
2002 and 2004 . Pneumococcal carriage rates were lower
in older adults in WA than Mackenzie et al. found in the
Northern Territory but too few samples were collected from
people aged ≥ 65 years in our study to enable accurate
comparison. Elsewhere in the world, studies in indigenous
populations and in developing countries have found
comparably high rates of pneumococcal carriage [16–18]. Risk
factors for high carriage rates in Australian Aboriginal people
including crowding and indoor smoking  were widespread
among our study participants.
Four of the 12 most common carriage serotypes (6C, 16F,
23B and 34) are not covered by any currently licensed vaccine
(Figure 3). Serotype 6C was the most frequently carried
serotype in our study (Table 2). In Alaska and the UK, carriage
of serotype 6A declined following 7vPCV programs, while the
proportion of 6C carriage isolates increased [7,19]. While data
on carriage of 6A in WA are not available for the pre-7vPCV
era, it is possible that a similar “replacement” took place
following the 7vPCV program, given that 6C was the most
commonly carried serotype in our study. Vaccination with
7vPCV, which includes 6B, elicits cross-reactive antibodies to
6A but does not appear to protect against disease caused by
6C [20,21]. Meanwhile Cooper et al. have reported that
13vPCV elicits cross-protective functional antibodies to 6C in
addition to covering 6A and 6B . We could expect that
carriage of serotype 6C may now decrease following the
introduction of the 13vPCV program for all children.
Serotype 16F has been one of the most common carriage
serotypes across Australia since the introduction of 7vPCV and
is a predominant cause of OM and tympanic membrane
perforation in Australian Aboriginal children . Serotype 19A
was the third most common serotype isolated in our study, and
was the most common serotype in children < 2 years of age.
We expect to see a reduction in carriage of 19A over the
coming years following the introduction of 13vPCV. Despite
their inclusion in 7vPCV, serotypes 23F and 19F were the
fourth and fifth most prevalent serotypes found in this study.
This was unexpected and requires monitoring over the coming
years to determine whether the 13vPCV program reduces
carriage of these serotypes. The high frequency of
nonserotypeable isolates circulating in the population warrants
close monitoring, and improved techniques are needed to
identify whether these are non-capsular strains or novel
23vPPV serotypes made up half (49.9%) of all serotypes
found in this study. 23vPPV was included on the immunization
schedule for Aboriginal children at 18 months of age and for
Aboriginal adults ≥ 55 years in WA. The relatively high
prevalence of 23vPPV serotypes in this study suggests it has
little effect on carriage. Outbreaks of IPD caused by serotypes
12F and 19A in 2010 and 2011 indicate 23vPPV may not have
been effective in preventing IPD or this may reflect the limited
Figure 3. Proportion of serotypeable pneumococci isolated from the nasopharynx between 2008 and 2011 that are
included in 7vPCV, 13vPCV, 23vPPV, or no currently licensed vaccine, by age group. A 7vPCV program was introduced in
2001 for all Aboriginal children. Specimens were collected prior to introduction of 13vPCV in July 2011.
Pneumococcal Carriage in Australian Aboriginals
PLOS ONE | www.plosone.org7 December 2013 | Volume 8 | Issue 12 | e82280
23vPPV coverage in WA [2,24]. We rarely identified serotypes
1 and 12F in the nasopharynx (Table 2), despite the outbreaks
of IPD due to these serotypes during the study period . It is
not possible to determine whether we were observing
replacement disease due to “vaccine pressure” or whether this
was part of the natural variation in incidence of these
serotypes. This could be expected due to the opportunistic
nature of our carriage surveillance resulting in swabs not being
collected at the time and in locations where serotype 1 or 12F
was circulating. Furthermore, serotypes 1 and 12F have high
invasive potential which suggests more transient carriage, so
they are rarely isolated from the nasopharynx even in very
large carriage studies [25–27].
Between 1999 and 2003 carriage rates were almost 50%
lower in non-Aboriginal children than in Aboriginal children in
the Kalgoorlie-Boulder cohort . During that time period
Aboriginal children began receiving 7vPCV while non-
Aboriginal children did not routinely receive 7vPCV until 2005.
More recently, between November 2007 and May 2009, a
cohort of 186 non-Aboriginal children < 36 months old
experiencing recurrent acute OM (rAOM) and 81 healthy
controls were recruited in a carriage study in WA. S.
pneumoniae, non-typeable H. influenzae and M. catarrhalis
were carried by 41%, 56% and 43% of the rAOM children and
26%, 19%, and 15% of controls . The carriage rates in both
the rAOM and control groups are considerably lower than we
found in Aboriginal children of the same age in this study.
Ongoing simultaneous surveillance of carriage in the Aboriginal
and non-Aboriginal populations is required to examine and
compare the effect of vaccination in both groups and give a
broad overview of carriage in the WA population. Surveillance
of bacterial nasopharyngeal carriage in non-Aboriginal children
< 5 years has recently begun in the metropolitan Perth area,
and will enhance our overview of carriage in the region.
Pneumococcal antibiotic resistance remains relatively
uncommon in this population apart from cotrimoxazole, which
is important when considering empiric therapy for common
infections such as OM and pneumonia. Reduced susceptibility
to penicillin was observed in one-quarter of isolates, but was
particularly common in nonserotypeable isolates that were also
more likely to be resistant to cotrimoxazole and erythromycin.
We compared our antibiotic susceptibility data with resistance
rates for 261 isolates (Lehmann et al., unpublished data) from
a cohort of 100 Aboriginal children born in Kalgoorlie-Boulder
and followed for 2 years between April 1999 and January 2003
. Cotrimoxazole resistance was more common in our
isolate collection (30.7% versus 22.6%, p = 0.01), but
susceptibilities to the other antimicrobial agents were not
significantly different. It will be important to continue to monitor
antibiotic susceptibility for the emergence of multi-resistant
Our study had some limitations. The opportunistic nature of
swab collection may not give a representative sample of the
population. Sampling in adults was biased towards women:
77% of adults aged over 20 years were female because
generally mothers and grandmothers accompanied their
children to medical services, where we had the opportunity to
ask them if they would like to participate in the study. However,
carriage rates were not significantly different in men and
women aged ≥ 20 years (p = 0.79). Vaccination data from
ACIR could only be accessed for 56.4% of children swabbed,
so our findings may not reflect the true number of vaccinated
children. The large expanse of land and diverse regions
covered by our surveillance could give rise to seasonal or
geographical variation in prevalence which we could not
ascertain as samples were frequently collected from limited
numbers of people living in many different communities visited
in different years and seasons.
Since July 2011, 13vPCV has replaced 7vPCV in the WA
immunization schedule. We therefore anticipate a shift in
serotype distribution, with a decrease in circulation of the six
additional 13vPCV serotypes now covered in the immunization
schedule. Over 30% of our isolates were 13vPCV serotypes. It
is essential to closely monitor changes in carriage and IPD
(rates, serotype distribution and antimicrobial susceptibility
patterns) over the coming years to ensure appropriate vaccine
policies are in place and to achieve the best outcome for the
WA Aboriginal population .
We thank all the participants involved in the study. We are
grateful to the communities and the staff of Aboriginal Medical
Services and Community Health Services who facilitated our
study visits and encouraged participation. We thank Kim Hare
for pneumococcal serotyping during the early period of the
study. We also thank Mr Joel Tan for his work on early data
management, and Professor Thomas Riley and Dr Lea-Ann
Kirkham for their helpful comments on the manuscript.
Conceived and designed the experiments: AH AL DL.
Performed the experiments: DC AH JB JJ NAS. Analyzed the
data: DC AH. Wrote the manuscript: DC AH PR DL.
1. World Health Organization (2012) Pneumococcal vaccines WHO
position paper - 2012. Weekly Epidemiological Record 87: 129-144.
2. Lehmann D, Willis J, Moore HC, Giele C, Murphy D et al. (2010) The
changing epidemiology of invasive pneumococcal disease in Aboriginal
and non-Aboriginal Western Australians from 1997 through 2007 and
emergence of nonvaccine serotypes. Clin Infect Dis 50: 1477-1486. doi:
10.1086/652440. PubMed: 20420501.
3. Lehmann D, Weeks S, Jacoby P, Elsbury D, Finucane J et al. (2008)
Absent otoacoustic emissions predict otitis media in young Aboriginal
children: A birth cohort study in Aboriginal and non-Aboriginal children
in an arid zone of Western Australia. BMC Pediatr 8: 32. doi:
10.1186/1471-2431-8-32. PubMed: 18755038.
4. Jacoby P, Carville KS, Hall G, Riley TV, Bowman J et al. (2011)
Crowding and other strong predictors of upper respiratory tract carriage
of otitis media-related bacteria in Australian Aboriginal and non-
Aboriginal children. Pediatr Infect Dis J 30: 480-485. PubMed:
5. Giele C, Moore H, Lehmann D, Waplington L, Keil AD et al. (2012)
Increase in invasive pneumococcal disease among the Western
Australian Aboriginal population due to non-vaccine serotypes, in
Pneumococcal Carriage in Australian Aboriginals
PLOS ONE | www.plosone.org8 December 2013 | Volume 8 | Issue 12 | e82280
particular serotype 1. p. 2012; 7th International Symposium on Download full-text
Pneumococci and Pneumococcal Diseases, Iguacu Falls, Brazil.
6. Weinberger DM, Harboe ZB, Flasche S, Scott JA, Lipsitch M (2011)
Prediction of serotypes causing invasive pneumococcal disease in
unvaccinated and vaccinated populations. Epidemiology 22: 199-207.
doi:10.1097/01.ede.0000392293.11358.8c. PubMed: 21646962.
7. Tocheva AS, Jefferies JMC, Rubery H, Bennett J, Afimeke G et al.
(2011) Declining serotype coverage of new pneumococcal conjugate
vaccines relating to the carriage of Streptococcus pneumoniae in young
children. Vaccine 29: 4400-4404. doi:10.1016/j.vaccine.2011.04.004.
8. Spijkerman J, van Gils EJ, Veenhoven RH, Hak E, Yzerman EP et al.
(2011) Carriage of Streptococcus pneumoniae 3 years after start of
vaccination program, the Netherlands. Emerg Infect Dis 17: 584–591.
doi:10.3201/eid1704101115. PubMed: 21470445.
9. Leach AJ, Morris PS, McCallum GB, Wilson CA, Stubbs L et al. (2009)
Emerging pneumococcal carriage serotypes in a high-risk population
receiving universal 7-valent pneumococcal conjugate vaccine and 23-
valent polysaccharide vaccine since 2001. BMC Infect Dis 9: 121. doi:
10.1186/1471-2334-9-121. PubMed: 19650933.
10. Australian Bureau of Statistics (2011) 2011 Census of Population and
11. Leach AJ, Stubbs E, Hare K, Beissbarth J, Morris PS (2008)
Comparison of nasal swabs with nose blowing for community-based
pneumococcal surveillance of healthy children. J Clin Microbiol 46:
2081-2082. doi:10.1128/JCM.00048-08. PubMed: 18385438.
12. Watson K, Carville K, Bowman J, Jacoby P, Riley TV et al. (2006)
Upper respiratory tract bacterial carriage in Aboriginal and non-
Aboriginal children in a semi-arid area of Western Australia. Pediatr
Infect Dis J 25: 782-790. doi:10.1097/01.inf.0000232705.49634.68.
13. Clinical and Laboratory Standards Institute (2007) Performance
Standards for Antimicrobial
Informational Supplement M100-S17. Wayne, PA, USA: CLSI.
14. Pai R, Moore MR, Pilishvili T, Gertz RE, Whitney CG et al. (2005)
Postvaccine genetic structure of Streptococcus pneumoniae serotype
19A from children in the United States. J Infect Dis 192: 1988-1995.
doi:10.1086/498043. PubMed: 16267772.
15. Mackenzie GA, Leach AJ, Carapetis JR, Fisher J, Morris PS (2010)
Epidemiology of nasopharyngeal carriage of respiratory bacterial
pathogens in children and adults: cross-sectional surveys in a
population with high rates of pneumococcal disease. BMC Infect Dis
10: 304. doi:10.1186/1471-2334-10-304. PubMed: 20969800.
16. Abdullahi O, Karani A, Tigoi CC, Mugo D, Kungu S et al. (2012) The
prevalence and risk factors for pneumococcal colonization of the
nasopharynx among children in Kilifi district, Kenya. PLOS ONE 7:
e30787. doi:10.1371/journal.pone.0030787. PubMed: 22363489.
17. Roca A, Bottomley C, Hill PC, Bojang A, Egere U et al. (2012) Effect of
age and vaccination with a pneumococcal conjugate vaccine on the
density of pneumococcal nasopharyngeal carriage. Clin Infect Dis 55:
816-824. doi:10.1093/cid/cis554. PubMed: 22700830.
18. Rivera-Olivero IA, Bogaert D, Bello T, del Nogal B, Sluijter M et al.
(2007) Pneumococcal carriage among indigenous Warao children in
Venezuela: serotypes, susceptibility
Susceptibility Testing: Seventh
patterns, and molecular
epidemiology. Clin Infect Dis 45: 1427-1434. doi:10.1086/522984.
19. Rudolph K, Bruce M, Bruden D, Zulz T, Wenger J et al. (2013)
Epidemiology of pneumococcal serotype 6A and 6C among invasive
and carriage isolates from Alaska, 1986–2009. Diagn Microbiol Infect
Dis 75: 271-276. doi:10.1016/j.diagmicrobio.2012.11.021. PubMed:
20. Park IH, Moore MR, Treanor JJ, Pelton SI, Pilishvili T et al. (2008)
Differential effects of pneumococcal vaccines against serotypes 6A and
6C. J Infect Dis 198: 1818-1822. doi:10.1086/593339. PubMed:
21. Väkeväinen M, Eklund C, Eskola J, Käyhty H (2001) Cross-reactivity of
antibodies to type 6B and 6A polysaccharides of Streptococcus
pneumoniae, evoked by pneumococcal conjugate vaccines, in infants.
J Infect Dis 184: 789-793. doi:10.1086/322984. PubMed: 11517443.
22. Cooper D, Yu X, Sidhu M, Nahm MH, Fernsten P et al. (2011) The 13-
valent pneumococcal conjugate vaccine (PCV13) elicits cross-
functional opsonophagocytic killing
Streptococcus pneumoniae serotypes 6C and 7A. Vaccine 29:
7207-7211. doi:10.1016/j.vaccine.2011.06.056. PubMed: 21689707.
23. Marsh RL, Smith-Vaughan H, Beissbarth J, Hare K, Kennedy M et al.
(2007) Molecular characterisation of pneumococcal serotype 16F:
Established predominant carriage and otitis media serotype in the
7vPCV era. Vaccine 25:
2006.09.016. PubMed: 17028080.
24. Menzies R, Turnour C, Chiu C, McIntyre P (2008) Vaccine preventable
diseases and vaccination coverage in Aboriginal and Torres Strait
Islander people, Australia 2003 to 2006. Communicable Diseases
Intelligence 32: S2-67. PubMed: 18711998.
25. Simell B, Auranen K, Käyhty H, Goldblatt D, Dagan R et al. (2012) The
fundamental link between pneumococcal carriage and disease. Expert
Rev Vaccines 11: 841-855. doi:10.1586/erv.12.53. PubMed: 22913260.
26. Brueggemann AB, Griffiths DT, Meats E, Peto T, Crook DW et al.
(2003) Clonal relationships
Streptococcus pneumoniae and
differences in invasive disease potential. J Infect Dis 187: 1424-1432.
doi:10.1086/374624. PubMed: 12717624.
27. Scott JR, Millar EV, Lipsitch M, Moulton LH, Weatherholtz R et al.
(2012) Impact of more than a decade of pneumococcal conjugate
vaccine use on carriage and invasive potential in Native American
communities. J Infect Dis 205: 280-288. doi:10.1093/infdis/jir730.
28. Wiertsema SP, Kirkham LA, Corscadden KJ, Mowe EN, Bowman JM et
al. (2011) Predominance of nontypeable Haemophilus influenzae in
children with otitis media following introduction of a 3+0 pneumococcal
conjugate vaccine schedule. Vaccine 29: 5163-5170. doi:10.1016/
j.vaccine.2011.05.035. PubMed: 21621576.
29. Lehmann D, Arumugaswamy A, Elsbury D, Finucane J, Stokes A et al.
(2008) The Kalgoorlie Otitis Media Research Project: rationale,
methods, population characteristics and ethical considerations.
Paediatr Perinat Epidemiol 22: 60-71. PubMed: 18173785.
30. Weinberger DM, Malley R, Lipsitch M (2011) Serotype replacement in
disease after pneumococcal vaccination. Lancet 378: 1962-1973. doi:
10.1016/S0140-6736(10)62225-8. PubMed: 21492929.
responses in humans to
between invasive and
Pneumococcal Carriage in Australian Aboriginals
PLOS ONE | www.plosone.org9December 2013 | Volume 8 | Issue 12 | e82280