Case-control Study of the Association Between Pertussis Vaccination in Infancy and the Risk of IgE-mediated Food Allergy
Conditions: Food Allergy
Sponsor: Telethon Kids Institute

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Estcourt MJ, et al. BMJ Open 2018;8:e020232. doi:10.1136/bmjopen-2017-020232
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Protocol for Pertussis Immunisation and 
Food Allergy (PIFA): a case–control 
study of the association between 
pertussis vaccination in infancy and the 
risk of IgE-mediated food allergy among 
Australian children
Marie J Estcourt,1,2 Julie A Marsh,1,3 Dianne E Campbell,4,5 Michael S Gold,6 
Katrina J Allen,7,8 Peter Richmond,1,9 Claire S Waddington,1,9 Thomas L Snelling1,10
To cite: Estcourt MJ, Marsh JA, 
Campbell DE, et al.  Protocol 
for Pertussis Immunisation and 
Food Allergy (PIFA): a case–
control study of the association 
between pertussis vaccination 
in infancy and the risk of IgE-
mediated food allergy among 
Australian children. BMJ Open 
2018;8:e020232. doi:10.1136/
bmjopen-2017-020232
►
►Prepublication history for 
this paper is available online. 
To view these files, please visit 
the journal online (http://​dx.​doi.​
org/​10.​1136/​bmjopen-​2017-​
020232). 
Received 3 November 2017
Accepted 27 November 2017
For numbered affiliations see 
end of article.
Correspondence to
Dr Thomas L Snelling;  
​Tom.​Snelling@​telethonkids.​
org.​au
Protocol
Abstract
Introduction  Atopic diseases, including food allergy, 
have become a predominant cause of chronic illness 
among children in developed countries. In Australia, a rise 
in hospitalisations among infants coded as anaphylaxis 
to foods coincided with the replacement of whole-cell 
pertussis (wP) vaccine with subunit acellular pertussis 
(aP) vaccine on the national immunisation schedule in 
the late 1990s. Atopy is characterised by a tendency 
to mount T helper type 2 (Th2) responses to otherwise 
innocuous environmental antigens. Compared with infants 
who receive aP as their first pertussis vaccine, those 
who receive wP appear less likely to mount Th2 immune 
responses to either vaccine or extraneous antigens. We 
therefore speculate that removal of wP from the vaccine 
schedule contributed to the observed rise in IgE-mediated 
food allergy among Australian infants.
Methods and analysis  This is a retrospective individually 
matched case–control study among a cohort of Australian 
children born from 1997 to 1999, the period of transition 
from wP to aP vaccines; we include in the cohort children 
listed on Australia’s comprehensive population-based 
immunisation register as having received a first dose 
of either pertussis vaccine by 16 weeks old. 500 cohort 
children diagnosed as having IgE-mediated food allergy at 
specialist allergy clinics will be included as cases. Controls 
matched to each case by date and jurisdiction of birth 
and regional socioeconomic index will be sampled from 
the immunisation register. Conditional logistic regression 
will be used to estimate OR (±95% CI) of receipt of wP (vs 
aP) as the first vaccine dose among cases compared with 
controls.
Ethics and dissemination  The study is approved 
by all relevant human research ethics committees: 
Western Australia Child and Adolescent Health Services 
(2015052EP), Women’s and Children’s Hospital (HREC/15/
WCHN/162), Royal Children’s Hospital (35230A) and 
Sydney Children’s Hospital Network (HREC/15/SCHN/405). 
Outcomes will be disseminated through publication and 
scientific presentation.
Trial registration number  NCT02490007.
Introduction
Epidemiology of atopic disease in Australia and 
internationally
As a group, atopic diseases (eczema, asthma, 
rhinoconjunctivitis and food allergy) are now 
the most prevalent chronic diseases of chil-
dren in resource-rich industrialised coun-
tries; at least one in four Australian children 
is affected by these conditions.1 Whereas 
the incidence of aeroallergic atopic diseases 
(asthma and rhinoconjunctivitis) began rising 
several decades ago and peaked in Australia 
in the 1980s,2 since the late 1990s a ‘second 
wave’ of non-aero allergic atopy has emerged 
characterised by severe IgE-mediated food 
Strengths and limitations of this study
►
►The transition from whole-cell pertussis  (wP) to 
acellular pertussis (aP) in Australia represents a 
natural experiment of the effect of infant pertussis 
vaccination on subsequent food allergy on a scale 
not achievable by a randomised controlled trial.
►
►The 
study 
is 
nested 
within 
Australia’s 
comprehensive, 
prospective, 
population-based 
immunisation register, meaning that ascertainment 
of vaccination status is likely to be accurate, and any 
misclassification is likely to be non-differential for 
cases and controls.
►
►We included only cases diagnosed as IgE-mediated 
food allergy in specialist tertiary allergy clinics.
►
►Not all children diagnosed with IgE-mediated 
food allergy had a formal food challenge, the 
gold standard for diagnosis.
►
►We assume that the probability of receipt of wP 
as the first pertussis vaccine dose (rather than aP) 
was dependent on date and jurisdiction of birth, but 
independent of any other risk factors for food allergy. 
It is not possible to verify if this assumption is valid.
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allergies in children.3 For example, one Australian allergy 
clinic observed a 12-fold rise in consultations for food 
allergy in children between 1995 and 2006.4 Fatal food 
anaphylaxis rose almost 10% per year from 1997 to 2013.5 
In the most comprehensive study of its kind, the preva-
lence of food sensitisation among 12-month-old Victorian 
infants was 18% (95% CI 17% to 19%), with 10% having 
challenge-proven food allergy.6 The most common aller-
gies were to peanut 3.0%, raw egg 8.9% and sesame 
0.8%. The prevalence of allergic eczema among infants 
was found to be even higher, 26.7% (95% CI 25.0% to 
28.4%).6 A similar phenomenon has also been described 
in the UK7 and the USA.8 9 A characteristic feature of this 
epidemic has been the onset of symptoms in early infancy 
and persistence of symptoms into adolescence.3 
The rise in atopic disease and sudden rise in food allergy, 
in particular, suggest one or more causal environmental 
triggers. It has been widely suggested that lifestyle change, 
in particular declining exposure to infection—the hygiene 
hypothesis10—is responsible. However, this does not by 
itself explain the more abrupt onset of food-related allergy 
in Australia.11
A temporal association exists between the onset of the 
epidemic of food allergies in Australia and the transi-
tion from the use of vaccines containing the whole-cell 
pertussis (wP) antigen to those containing the acellular 
pertussis (aP) antigen. Use of aP began to replace that of 
wP in the mid-1990s and by early 1999; most scheduled 
childhood pertussis vaccines were aP.12 In the USA and 
in the UK, a temporal association between the phasing 
out of wP vaccines and the increase in hospitalisations 
for food allergy is not clear (unpublished data, personal 
communication) although coding of hospitalisation 
records for allergies may be both insensitive and non-spe-
cific so any associations could be easily obscured. In light 
of the contrasting immunological effects of wP compared 
with aP (reviewed below), it is plausible that a causal rela-
tionship underlies the ecological association observed in 
Australia.
Immunological basis of atopic disease
A reciprocal relationship exists between T helper cell type 
1 and type 2 (Th1 and Th2) immunity due to cross-reg-
ulation of their respective effector cell populations.13 
The balance between Th1 and Th2 is established during 
early infancy. Atopy is caused by a dysregulation of this 
balance in the developing immune system, characterised 
by an immune phenotype that is heavily biased towards 
Th2 immunity or ‘Th2 polarised’, the consequent over-
production of IgE to one or more allergens, and IgE-me-
diated inflammation.
The developing immune system appears most suscep-
tible to Th2 polarisation in the critical early months 
after birth. This period is pivotal in the transition from 
the Th1-suppressed/Th2-dominant phenotype needed 
to avoid rejection in utero, to a more Th1 /Th2-bal-
anced phenotype. Newborns are exposed to an array of 
new antigenic proteins from infection and other natural 
environmental exposures, including gut flora and food 
components. The development of tolerance to these 
natural exposures represents an early challenge to the 
developing immune system. It appears that  the devel-
opment of tolerance can be influenced by a range of 
factors, which in turn modify the risk of food allergy. The 
best studied of these are optimal bacterial colonisation, 
breast milk, prebiotics, vitamins and polyunsaturated fatty 
acids14; however, so far no broadly effective strategies have 
been identified to promote the natural development of 
Th1/Th2 balance or to prevent the development of 
food-related and other allergies in infants.
Immune profile of pertussis vaccines
Th1 responses are needed for clearing pertussis infec-
tion.15 wP stimulates these adaptive responses via the pres-
ence of bacterial cell wall components which stimulate the 
Th1 immune pathway.16 Stimulation of the Th1 pathway 
also results in local and systemic adverse vaccine reactions, 
which was the driving reason for phasing out use of wP. 
In contrast, aP typically induces strong Th2 responses15–17 
with the production of antigen-specific antibodies. While 
this aP response provides immediate antibody-derived 
protection from disease, the absence of Th1 stimulation 
may skew the developing immune response towards one 
characterised by Th2 responses. Children who receive at 
least one dose of wP in infancy appear better protected 
against pertussis than children who receive aP only.18 The 
most recent meta-analysis of vaccine efficacy comparing 
wP and aP estimates efficacy at 94% (95% CI 88% to 97%) 
and 84% (95% CI 81% to 87%), respectively.19 Moreover, 
a number of studies detail the Th2 immune bias induced 
in some infants who received aP-only schedules, resulting 
in excessive IgE production against vaccine antigens.20 21 
A recent study has shown that the Th polarisation induced 
by infant immunisation can persist into adolescence 
and adulthood and is maintained after booster vacci-
nation.22 This could be due to the combined effect of: 
(1) carry over of the Th2-biased in utero phenotype, (2) 
the presence of alum and pertussis toxin, which have 
Th2-adjuvantising properties and (3) the absence of the 
balancing Th1-stimulating ligands present in wP. These 
effects manifest especially among children with evidence 
of an underlying Th2-skewed phenotype.20 21
Broader immunomodulating properties of pertussis
The Th2 polarising effect of the initial dose of aP appears 
to extend beyond vaccine-specific responses; there may 
be a significant ‘bystander’ effect with upregulation of 
circulating IgE to a broad range of antigens following 
subsequent doses of aP. Importantly, these Th2-stimula-
tory effects appear to extend to food allergens,23 espe-
cially in early infancy when immune memory against 
allergens is most susceptible to programming.24 25 The 
administration of additional pertussis vaccine doses in 
later childhood in children primed with aP only is asso-
ciated with frequent injection-site reactions. In Australia, 
this contributed to the removal of the 18-month-old 
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pertussis booster given in 2003, which in turn led to 
reduced protection against pertussis among preschool 
aged children.26 These adverse reactions have been 
linked to the presence of high levels of vaccine-specific, 
Th2-polarised, Th-memory cells.27 Children primed with 
aP  only also exhibit high titres of total IgE, including 
tetanus (T)-specific28 29 and pertussis-specific IgE.28 These 
responses are rarely observed among children who have 
received wP-containing vaccines, including those who 
have received mixed vaccine schedules of wP and aP.30 
A recent study of a birth cohort examined the effect of 
delaying aP vaccination on atopic outcomes. This study 
found that delay of aP by 1 month resulted in a reduction 
in eczema in infants and use of eczema medications.31 
To date, no other studies have found a relationship 
between aP vaccines and allergy. A study from the 1990s 
found no significant difference in overall rates of skin 
prick test  (SPT) reactivity or allergic disease among 
young Swedish children who received wP compared with 
those who received aP.32 In that study population, the 
frequency of food allergy was low (~2%) compared with 
that observed among contemporary Australian infants. A 
more recent prospective birth cohort of children from 
the Isle of Wight also failed to find any difference in the 
frequency of atopic outcomes among children receiving 
wP versus aP.33
Based on these observations, we speculate that removal 
of wP from the infant vaccine schedule has contributed 
to the observed rise in IgE-mediated food allergy among 
Australian infants.
Aim
To assess the possible food allergy-preventive benefit of 
using wP compared with aP for pertussis vaccination in 
childhood.
Objectives and outcome measures
Primary objective
To determine if Australian children born between 1997 
and 1999 (inclusive) who received wP as their first 
pertussis vaccine dose in infancy were less likely to subse-
quently develop IgE-mediated food allergy compared 
with contemporaneous children who received aP as their 
first pertussis vaccine dose.
Secondary objectives
1.	 To determine if Australian children born in the years 
1997 to 1999 (inclusive) who received at least one 
dose of a wP vaccine at any age were less likely to sub-
sequently develop IgE-mediated food allergy com-
pared with contemporaneous children who received 
only aP vaccines.
2.	 To determine if Australian children born in the 
years 1997 to 1999 (inclusive) who received wP vac-
cines exclusively were less likely to subsequently 
develop IgE-mediated food allergy compared with 
contemporaneous children who received only aP 
vaccines.
Prespecified hypotheses
Primary hypothesis 
Among Australian children with documented evidence of 
receiving a pertussis vaccine before age 16 weeks, a record 
of receipt of a wP vaccine as dose one is less common than 
aP vaccine among those subsequently diagnosed with 
food allergy compared with date of birth, socioeconomic 
index and jurisdiction-matched cohort controls.
Secondary hypothesis I
Among Australian children with documented evidence of 
receiving a pertussis vaccine before age 16 weeks, a record 
of receipt of at least one dose of wP vaccine at any age is less 
common than aP vaccine at all ages among those subse-
quently diagnosed with food allergy compared with date 
of birth, socioeconomic index and jurisdiction-matched 
cohort controls.
Secondary hypothesis II
Among Australian children with documented evidence 
of receiving a pertussis vaccine before age 16 weeks, a 
record of receipt of one or more wP vaccine doses exclu-
sively (ie, no aP vaccine) is less common than one or 
more aP vaccine doses exclusively (ie, no wP vaccines) 
among those subsequently diagnosed with food allergy 
compared with date of birth, socioeconomic index and 
jurisdiction-matched cohort controls.
Methods and analysis
Study design
This is a retrospective individually matched case–control 
study of Australian children born during the period of 
transition from use of wP-containing pertussis vaccines 
to aP-containing pertussis vaccines (year of birth 1997–
1999 inclusive) and who are registered on the Australian 
Immunisation Register (AIR; prior to 2016 known as the 
Australian Childhood Immunisation Register) and who 
have received their first dose of pertussis vaccine before 
age 16 weeks. Cases are drawn from private allergy clinics 
and allergy clinics associated with tertiary teaching hospi-
tals around Australia. Five hundred children identified 
as having IgE-mediated food allergy, from reviewing case 
histories against standardised inclusion criteria, will be 
enrolled. Cohort controls will be drawn from a deiden-
tified database of the AIR held by the National Centre 
for Immunisation Research and Surveillance of Vaccine 
Preventable Diseases. Each case will be individually 
matched with up to 10 cohort controls based on year of 
birth, socioeconomic index and jurisdiction.
Project coordination and epidemiological analysis is 
conducted from the Wesfarmers Centre of Vaccines and 
Infectious Diseases at the Telethon Kids Institute Western 
Australia.
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Primary outcome measure
The primary outcome is IgE-mediated food allergy diag-
nosed by a registered specialist paediatric allergist.
Definition of exposure of interest (vaccination)
For the primary analysis, exposure is defined as 
AIR-documented receipt of either a wP-containing 
vaccine or receipt of an aP-containing vaccine as the 
first vaccine against pertussis and given before age 16 
weeks (strictly <112 days) irrespective of any subsequent 
pertussis vaccinations.
For the secondary analyses, exposure is defined as 
either:
1.	 AIR-documented receipt of one or more doses of wP at 
any age or only aP-containing vaccines for all pertus-
sis vaccinations. All other sequences of vaccines will 
be coded as non-applicable and excluded from the 
analysis.
2.	 AIR-documented receipt of only wP-containing vac-
cine for all pertussis vaccinations or only aP-contain-
ing vaccines for all pertussis immunisations. All other 
sequences of vaccines will be coded as non-applicable 
and excluded from the analysis.
Vaccination status for each case and its corresponding 
matched controls is referenced from the age of allergy 
diagnosis in the case.
Study setting
Cases are drawn from private allergy clinics and from 
allergy clinics associated with tertiary teaching hospi-
tals in the Australian states of New South Wales (NSW), 
Victoria, South Australia and Western Australia; matched 
cohort controls are selected from among children regis-
tered as resident in the same state and recorded as having 
received at least one pertussis vaccine dose on the popu-
lation-based vaccine register (AIR).
Participant identification
Eligibility criteria
All cases and cohort controls must be registered on AIR as 
having had a first dose of any pertussis-containing vaccine 
before age 16 weeks and during the period in which the 
transition from wP to aP vaccine occurred: 1 January 1997 
to 31 December 1999.
Overall description of trial participants
To maximise the study efficiency in the case, identifi-
cation has been concentrated among children born 
when aP accounted for between 25% and 75% of infant 
vaccine doses administered. The changeover from wP 
to aP occurred with slightly different timing in the 
different jurisdictions of Australia so the exact dates 
vary across jurisdictions. In the first instance, cases have 
been identified from among clinic attendees in NSW, 
Victoria, Queensland and Western Australia who are 
AIR-registered and born from 1 October 1998 to 30 
June 1999. For South Australia, cases have been drawn 
from AIR-registered children born from 1 July 1997 to 
30 October 1998 owing to the earlier uptake of aP in 
that state.
Five  hundred cases in total will be enrolled. If fewer 
than 500 cases are identified from among children 
born within the initial birthdate range, CI will expand 
this birthdate range for NSW, Victoria, Queensland and 
Western Australia to 1 June 1998–30 October 1999; for 
South Australia, the birthdate range will be  expanded 
to 1 April 1997–30 April 1999. If there are still insuffi-
cient eligible cases identified, the birthdate range will be 
progressively increased by 3-month increments in each 
direction for all jurisdictions until 500 cases are identified 
or until the limits of 1 January 1997 and 31 December 
1999 are reached (whichever occurs first).
Case definition
Cases are considered to have IgE-mediated food allergy 
on the basis of (1) a documented history of consistent 
clinical symptoms following ingestion of an implicated 
food and (2) evidence of sensitisation to that food via 
either positive SPT or elevated-specific IgE to the impli-
cated food, with onset after the first pertussis-containing 
vaccine but before age 15 years.
To meet the case definition of IgE-mediated food 
allergy, the case must satisfy BOTH:
The clinical notes or a clinical letter arising from the 
allergy consult explicitly documents the presence of one 
or more of the following features:
1.	 urticaria
2.	 angioedema
3.	 emesis
4.	 vocal hoarseness
5.	 persistent cough
6.	  wheeze
7.	 stridor
8.	 collapse
9.	 hypotension
with onset of at least one feature within 1 hour of 
ingestion of the suspected food where this can reason-
ably be inferred from statements such as ‘immediate’ or 
‘within x minutes’ where x is <60
AND
Documented evidence of allergic sensitisation to the 
implicated food through EITHER:
1.	 specific IgE positive to suspected food (serum-specific 
IgE >0.35 kU/L)
2.	 positive SPT to suspected food (weal diameter >3 mm)
where evidence of sensitisation must be at the time 
of consultation or within 6 months after the clinical 
encounter.
Other acceptable terms:
When reviewing case histories, the below terms are 
considered synonymous:
1.	 urticaria—hives, rash, welts
2.	 angioedema—oedema, swelling of lips or eyes
3.	 emesis—vomit or vomiting
4.	 vocal hoarseness—horse voice, raspy voice
5.	 persistent cough
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6.	  wheeze
7.	 stridor
8.	 collapse—faint, loss of consciousness
9.	 hypotension—low blood pressure.
The case definition has been agreed on by specialist aller-
gists associated with the study as consistent with interna-
tional expert consensus for the definition of IgE-mediated 
food allergy.
Determination of exposure (vaccination)
The primary exposure of interest for cases and cohort 
controls is the first received pertussis vaccine as recorded 
on the AIR. The Australian vaccination schedule 
recommends three sequential priming vaccines against 
pertussis at approximately 2, 4 and 6 months of age. 
Cases and controls will have either received aP or wP 
together with T and diphtheria, either with or without 
hepatitis B as part of commercially combined vaccine 
preparations. All children will have been eligible for 
booster doses of aP at age 18 months old and at age 4 
years old.
Ethics and dissemination
A waiver of consent was sought and approved on the 
basis that the study poses negligible risk to participants 
and that seeking individual consent for access to data 
was unfeasible and may lead to ascertainment bias.
Statistics
Sample size and power considerations
A study involving 500 sets of cases and controls, with 
10 matched controls for each case, has 80% power to 
detect a 23% lower risk (OR 0.77) of food allergy among 
children who received wP as their first dose of pertussis 
vaccine compared with those who received aP as their 
first dose. This assumes that: (1) 50% of cohort controls 
receive a first pertussis vaccine dose of wP on average, 
(2) the correlation coefficient for exposure (first dose 
of wP) between cases and matched controls is 0.5 and 
(3) a two-sided significance level of 5%. We believe that 
a smaller effect size will not influence vaccine policy.
Bias
Management of confounding
Since routine vaccines in Australia are delivered almost 
exclusively via the National Immunisation Programme, 
date of birth (and therefore date of vaccination) and 
jurisdiction are considered to be the only relevant factors 
associated with vaccine type received (wP vs aP) and, 
therefore, the only relevant potential confounders. We 
will minimise confounding by these factors by direct 
matching. In so far as the type of vaccine received is 
expected to be independent of ethnicity, sex, family size, 
birth order, pet ownership and all other factors putatively 
or known to be related to food allergy, there are unlikely 
to be any other relevant confounders of the association 
between vaccine type and allergy; inability to match or 
adjust for other factors poses negligible threat to study 
validity.
Minimising information bias
The case definition is intended to be pragmatic and 
yet specific for IgE-mediated food allergy, excluding 
many non-allergic food reactions potentially misclassi-
fied as allergy by non-specialists and inhospital coding. 
For completeness, we will conduct an a priori sensitivity 
analyses which will include as cases only those children 
meeting the case definition who also have (1) chal-
lenge-proven food allergy and (2) evidence of sensitisa-
tion at or higher than the following levels: SPTs: 8 mm for 
cow milk, 7 mm for egg and 8 mm for peanut or IgE serum 
responses: 15  kU/L for cow milk, 7 kU/L for egg  and 
14 kU/L for peanut. These are the documented levels for 
95% positive predictive value (PPV) as defined by Sporik 
et al34 and Sampson.35 Ascertainment of vaccination status 
will be from the AIR for both cases and controls and will 
not rely on either parental recall or recording in medical 
records. The AIR record of cases will only be ascertained 
after verification from the site Principle Investigator (PI) 
that the case definition is fully met. Children with food 
allergy will be excluded as cases if they are not registered 
on AIR. There is no reason to expect that the accuracy 
or completeness of AIR should be different for cases and 
controls, so any inaccuracy is likely to be non-differential.
Minimisation of selection bias
Cases are sampled only from among children presenting 
to specialist-led private allergy clinics and allergy clinics 
at tertiary paediatric centres. To ensure correct classifica-
tion of cases, we will not sample cases from non-tertiary 
Australian hospitals, from cases diagnosed and managed 
by non-specialists or those without confirmation of 
sensitisation. We nonetheless expect cases will be gener-
ally representative of all Australian children with true 
IgE-mediated food allergy in the birth cohort. Cohort 
controls will be sampled from date of birth, jurisdiction 
and socioeconomic index-matched children from the 
AIR, a comprehensive population-based register of all 
Medicare-registered children in Australia. Since cohort 
controls are sampled at random, they will provide an unbi-
ased estimate of the vaccine status of the baseline source 
population for each case by date of birth, jurisdiction and 
Index of Relative Socio-economic Advantage and Disad-
vantage (IRSAD) score (Australian Bureau of Statistics 
(ABS) -assigned socioeconomic index by postcode).
Description of statistical methods
The study population characteristics will be summarised 
by case or control status using frequency and propor-
tion for categorical or binary variables, means and SDs 
for symmetric continuous distributions and medians and 
IQRs for asymmetric distributions. Conditional logistic 
regression will be used to perform hypothesis tests of the 
association between pertussis vaccine type (wP or aP) and 
IgE-mediated food allergy. Results will be summarised 
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using ORs and presented with associated 95% CIs. Since 
controls will be sampled from the AIR irrespective of past 
or future case status, the OR will be considered to be an 
unbiased estimator of the relative risk of food allergy 
among children receiving wP compared with aP vaccine.
Analysis of outcome measures
Primary analysis population
 All case and control individuals recorded on the AIR as 
receiving at least one dose of pertussis vaccine before age 
16 weeks will be included in the primary analysis, irre-
spective of whether they received any further doses of 
pertussis vaccine.
Primary analysis
 Conditional logistic regression will be used to evaluate 
the association between receipt of wP versus aP as the 
first pertussis vaccine and diagnosis of IgE-mediated food 
allergy. Direct matching will be on date of birth (+/−7 
days), jurisdiction (Australian state or territory) and 
IRSAD decile of the most recent Medicare-listed postcode 
(1st to 10th); no factors or interactions will be adjusted 
for in the a priori analysis.
For the primary analysis, a child’s exposure will be 
coded as either:
aP1: first pertussis vaccine dose of aP, with subsequent 
doses either wP or aP or none
or
wP1: first pertussis vaccine dose of wP, with subsequent 
doses either wP or aP or none.
The comparison of primary interest will be between 
aP1 and wP1 vaccinated children.
Secondary analysis population
  As for the primary analysis population, however, the 
comparison of wP-only and aP-only vaccinated children 
(secondary analysis II) will exclude any children who 
received a mixture of aP and wP vaccines.
Secondary analysis
  As for the primary analysis to evaluate the association 
between pertussis vaccines received (wP  only or mixed 
wP/aP in any combination, compared with aP only) and 
IgE-mediated food allergy.
For secondary analyses: (1), a child’s exposure will be 
coded as either:
 aP_only: all pertussis vaccine doses as aP, none as wP
or
wP_mix: at least one dose of wP at any age.
The comparison of interest is between aP only and at 
least one dose of wP vaccine.
For secondary analyses: (2), a child’s exposure will also 
be coded as either:
aP_only: all pertussis vaccine doses as aP, none as wP
or
wP_only: all pertussis vaccine doses as wP, none as aP.
The comparison of interest is between aP-only and 
wP-only vaccinated children. All mixed aP/wP vacci-
nated children will be excluded from the analysis. Table 1 
provides a summary of the coding of exposure for the 
primary and secondary analyses.
Any analyses other than those outlined above or in the 
sensitivity analyses and case subgroup analysis below will 
be declared as unplanned and post hoc.
Matching procedures
For each identified case, up to 10 children will be 
randomly sampled without replacement from the AIR 
database from among all children born on the same 
day as the case ±7 days and from the same jurisdiction 
and from a postcode with the same IRSAD decile (1st to 
10th). Children will only be included once as a case. Each 
cohort control will be associated with one unique case. 
Consistent with the case–cohort method,36 sampling of 
controls will be from the register cohort without regard 
to case status (ie, children will be eligible to be a control 
irrespective of whether they are at any stage a case). In 
Table 1  Summary of the coding of exposure for the primary and secondary analyses
First dose,
study eligibility requires 
first dose before age 
16 weeks
Second dose
Third dose
Primary coding,
first wP versus 
first aP
Secondary (1) coding,
any wP versus only aP
Secondary (2) coding,
only wP versus only aP
wP
Missing
Missing
wP1
wP_mix
wP_only
wP
wP
Missing
wP1
wP_mix
wP_only
wP
wP
wP
wP1
wP_mix
wP_only
wP
aP
aP or missing
wP1
wP_mix
Not included
wP
aP or missing
aP
wP1
wP_mix
Not included
aP
wP or missing
wP
aP1
wP_mix
Not included
aP
wP
wP or missing
aP1
wP_mix
Not included
aP
aP
aP
aP1
aP_only
aP_only
aP
aP
Missing
aP1
aP_only
aP_only
aP
Missing
Missing
aP1
aP_only
aP_only
aP, acellular pertussis; wP, whole-cell pertussis.
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total, up to 5000 controls will be sampled. IRSAD deciles 
will be ascertained from ABS data from the 2011 census 
since it is likely that only the most recent Medicare post-
code is available for the majority of the participants.
Sensitivity analysis
In the first instance, a sensitivity analysis will be performed 
on the case definition for the primary analysis based on 
confirmation of food allergy via a food challenge. Confir-
mation by food challenge is considered the gold standard 
for food allergy, but in clinical practice, this has more 
usually been reserved for cases in which there is diagnostic 
uncertainty or to confirm resolution of the food allergy. 
If there is a significant change in the interpretation of the 
results based on the sensitivity analysis compared with the 
primary analysis, then further sensitivity analyses will also 
be performed for the secondary analyses.
As an additional sensitivity analysis, the case definition 
will require documentation of an SPT weal of 8 mm for 
cow milk, 7 mm for egg or 8 mm for peanut or food-spe-
cific serum IgE of 15 kU/L for cow milk, 7 kU/L for egg 
or 14 kU/L for peanut. These more conservative cutoffs 
correspond to almost 100% and 95% PPV of IgE-medi-
ated allergy for the SPT and ss-IgE, respectively.
Case subgroup analysis
To investigate the potential heterogeneity of responses 
following exposure to specific vaccine formulations, we 
will conduct an a priori subgroup analysis by acellular 
vaccine brand (excluding children who have received 
mixed acellular vaccine types). All other subgroup anal-
yses will be declared as unplanned and post hoc.
Discussion
Allergy represents a significant disease burden in devel-
oped countries. The temporal association between an 
apparent increase in severe food allergy and the replace-
ment of whole cell with aP vaccine in Australia warrants 
further investigation. Food allergy is not only important 
in its own right, it is also associated with eczema and with 
asthma (fourfold increased risk) in later childhood.37 38
This study has been designed to comply with both the 
Strengthening the Reporting of Observational Studies 
in Epidemiology recommendations and also the more 
specific recommendations put forward by Sharpe et al39 
for case–cohort studies. The strengths of this study include 
objective allergy definition and access to an established 
prospective population-based vaccine register for deter-
mination of vaccination status of both cases and cohort 
controls. Access to patient lists of allergist-diagnosed food 
allergy from large paediatric referral centres along with 
detailed prospectively collected immunisation records 
from the AIR provides a unique opportunity to investi-
gate a potential relationship between these events. The 
transition from wP to aP in Australia represents a natural 
experiment of the effect of infant wP on subsequent 
food allergy, on a scale unachievable by a randomised 
controlled trial.
The disadvantages of this study are that it is reliant on 
existent databases for which there is little way to assess 
the validity or accuracy of data entry. The AIR database 
has been lauded as a highly effective means of tracking 
vaccination in the Australian population; however, there 
is evidence of under-reporting of administered vaccines,40 
and there has been no validation of the quality of data 
entry into the database. Finally, we assume that the type 
of pertussis vaccine administered was dependent on juris-
diction and date of birth, but not otherwise dependent 
on factors which are also risk factors for allergy. While this 
assumption appears entirely reasonable, we are not able 
to assess its validity.
Author affiliations
1Wesfarmers Centre of Vaccines & Infectious Diseases, Telethon Kids Institute, West 
Perth, Western Australia, Australia
2School of Population and Global Health, University of Western Australia, Crawley, 
Western Australia, Australia
3Centre for Applied Statistics, University of Western Australia, Crawley, Western 
Australia, Australia
4Department of Allergy and Immunology, The Children’s Hospital at Westmead, 
Westmead, New South Wales, Australia
5Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
6School of Medicine, University of Adelaide, Women’s and Children’s Health 
Network, North Adelaide, South Australia, Australia
7Centre for Food and Allergy Research, Murdoch Children’s Research Institute, 
Melbourne, Australia
8Department of Paediatrics, University of Melbourne, Royal Children’s Hospital 
Melbourne, Victoria, Australia
9Child Health Research, Princess Margaret Hospital for Children, Subiaco, Western 
Australia, Australia
10School of Public Health, Curtin University, Bentley, Western Australia, Australia
Contributors  TLS, MSG, DEC, KJA and CSW were responsible for study concept, 
design and funding acquisition. MJE, TLS, CSW and JAM wrote the protocol. MJE 
drafted the manuscript and coordinated manuscript preparation and revision. 
DEC, MSG, KJA and PR specified the clinical definition of food allergy for the study. 
JAM and TLS developed the statistical analysis plan. All authors provided critical 
evaluation and revision of the manuscript and have given final approval of the 
manuscript accepting responsibility for all aspects.
Funding  This work was supported by Australian National Health and Medical 
Research Council (NHMRC) project grant fund no 1079753. MJE is supported by a 
postgraduate scholarship through the Centre for Food Allergy Research, Australia. 
TLS holds an NHMRC Career Development Fellowship (no 1111657) and a Raine 
Clinical Research Fellowship. 
Competing interests  None declared.
Patient consent  Not required.
Ethics approval  This study was approved by the Human Research Ethics 
Committees (HREC) in each jurisdiction. The PIFA study is approved by the Child 
and Adolescent Health Service Human Research Ethics Committee, Perth, Western 
Australia (ref 2015052EP), Adelaide Women’s and Children’s Hospital HREC, South 
Australia (ref HREC/15/WCHN/162), Royal Children’s Hospital HREC, Victoria, 
Australia (ref 35230A) and Sydney Children’s Hospital Network HREC, New South 
Wales, Australia (ref HREC/15/SCHN/405). 
Provenance and peer review  Not commissioned; peer reviewed for ethical and 
funding approval prior to submission.
Open Access This is an Open Access article distributed in accordance with the 
Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits 
others to distribute, remix, adapt, build upon this work non-commercially, and license 
their derivative works on different terms, provided the original work is properly cited 
and the use is non-commercial. See: http://​creativecommons.​org/​licenses/​by-​nc/​4.​0/
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© Article author(s) (or their employer(s) unless otherwise stated in the text of the 
article) 2018. All rights reserved. No commercial use is permitted unless otherwise 
expressly granted.
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children
IgE-mediated food allergy among Australian 
vaccination in infancy and the risk of
the association between pertussis 
control study of
−
Food Allergy (PIFA): a case
 
Protocol for Pertussis Immunisation and
Snelling
Katrina J Allen, Peter Richmond, Claire S Waddington and Thomas L 
Marie J Estcourt, Julie A Marsh, Dianne E Campbell, Michael S Gold,
doi: 10.1136/bmjopen-2017-020232
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