An Observational Cross-sectional Study to Assess Oropharyngeal Carriage of N. Meningitidis in South Australian School Leavers
Conditions: Neisseria Meningitidis
Sponsor: University of Adelaide

Study to Assess Oropharyngeal Carriage of N. Meningitidis in South Australian School 
Leavers.  
Clinicaltrials.gov: NCT03419533 
Protocol V5, 7th November 2017 

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PHASE 2: AN OBSERVATIONAL CROSS SECTIONAL STUDY 
TO ASSESS NASOPHARYNGEAL CARRIAGE OF N. 
MENINGITIDIS IN SOUTH AUSTRALIAN UNIVERSITY 
STUDENTS AND SCHOOL LEAVERS  
 
PHASE 2 (STUDY PART 2 AND STUDY PART 3) PROTOCOL SUMMARY 
Title: 
South Australian Men B vaccine herd immunity study. 
Study Part 2: Pilot observational longitudinal study to assess nasopharyngeal 
carriage of Neisseria meningitidis in South Australian university students  
Study Part 3: An observational cross sectional study to assess nasopharyngeal 
carriage of Neisseria meningitidis in South Australian school leavers.   
Précis: 
To estimate the prevalence of N. meningitides in first year university students 
and school leavers in South Australia posterior oro-pharyngeal swabs will be 
obtained prior to and post  implementation of the school immunisation program 
(Phase 1). Potential risk factors will be assessed along with a comparison of 
carriage prevalence in vaccinated and unvaccinatedparticipants. Carriage will be 
estimated at baseline (2017) and in 2018, 2019  and potentially additionally in 
2020 if funding available (post implementation of the school immunisation 
program (Phase 1). 
Objectives: 
 
Study Part 2: 2017 Pilot Longitudinal Carriage Study 
 Primary Objective  
 
Estimate the carriage prevalence of all genogroups of N. meningitidis in 
South Australian first year university students.  
Secondary Objectives  
 
Estimate the carriage prevalence of N. meningitidis genogroups causing 
disease (A, B, C, W, X, Y) in South Australian first year university students. 
 
Identify characteristics associated with carriage prevalence of all N. 
meningitidis  genogroups in South Australian first year university students. 
 
Estimate the change in carriage prevalence of all genogroups of N. 
meningitidis in South Australian first year university students at baseline 
(first week of university) and 3 months later Estimate any difference in PCR 
positivity after freezing of the sample at 6, 16  and 48 hours post 
collection.Estimate any difference in positivity of isolates determined by 
culture after freezing of samples at 6, 16 and 48 hours post collection 
Study Part 3: 2018 /2019 /2020 Cross-sectional carriage study 
Primary Objective  
 
Estimate the difference in carriage prevalence of disease causing genogroups 
of N.meningitidis (A, B, C, W, X, Y) in South Australian school leavers in 2018 
(year 12 in 2017), 2019 (year 12 in 2018) and 2020 (year 12 in 2019)following 
implementation of a school immunisation program in year 10, 11 and 12 
South Australian students from 2017-2018. 

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Secondary Objectives  
 
Estimate the difference in carriage prevalence of all N. meningitidis 
genogroups in South Australian school leavers in 2018 (year 12 in 2017),2019 
(year 12 in 2018) and 2020 (year 12 in 2019)  following implementation of a 
school immunisation program in year 10, 11 and 12 South Australian 
students from 2017-2018. 
 
Estimate the difference in carriage prevalence of each N. meningitidis 
genogroup (A, B, C, W, X, Y) in South Australian school leavers in 2018 (year 
12 in 2017), 2019 (year 12 in 2018) and 2020 (year 12 in 2019)  following 
implementation of a school immunisation program in year 10, 11 and 12 
South Australian students from 2017-2018. 
 
Estimate the difference in carriage prevalence of all N. meningitidis 
genogroups in South Australian school leavers  who have received Bexsero ®  
compared to unvaccinated students.Estimate the difference in carriage 
prevalence of N. meningitidis genogroups causing disease (A, B, C, W, X, Y)  
in South Australian school leavers  who receivedBexsero ® , compared to 
unvaccinated students. 
 
Estimate the difference in each N. meningitidis genogroup carriage 
prevalence in South Australian school leavers who received Bexsero ®, 
compared to unvaccinated students. 
 
Identify characteristics associated with carriage prevalence of all N. 
meningitidis genogroups in South Australian school leavers in 2018 / 2019/ 
2020. 
 
Identify characteristics associated with carriage prevalence of N. 
meningitidis genotypes causing disease (A, B, C, W, X, Y) in South Australian 
school leavers in 2018 /2019 /2020. 
Primary Endpoint 
The pilot study describing baseline carriage in South Australian university 
students will be completed in 2017.  
Carriage prevalence of N. meningitidis as determined by PCR  
Population: 
South Australian first year university students and school leavers.  
Study Duration: 
The study recruitment will commence in 2017 with independent cohorts 
recruited over a three year period.  
Participant Duration: 
Study Part 2: The pilot study has two time points with the total duration being 
about 3 months. Study Part 3: The participants have no ongoing involvement 
following a pharyngeal swab at visit 1.  
 

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STUDY PARTS 2 AND 3 SCHEMATIC OF STUDY DESIGN 
 
 
 
 
 
Obtain informed consent. Screen subjects by inclusion/exclusion criteria 
2020 Single arm 
first year school 
leavers 
2017 Single arm 
first year uni 
students  
2018 Single arm 
 first year school 
leavers 
2019 Single arm 
 first year school 
leavers 
Complete baseline questionnaire  
Collect baseline posterior pharyngeal swab 
End of 
follow up 
Complete 
questionnaire. 
Collect posterior 
pharyngeal swab 3 
months after first visit. 
End of 
follow up 
End of 
follow up 
End of 
follow up 

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1 
KEY ROLES 
Study collaborating organisations  
 
University of Adelaide, Adelaide SA (Sponsor) 
Vaccinology and Immunology Research Trials Unit, Women’s and Children’s Hospital, Adelaide, SA (co-
ordination & HREC) 
 
SA Pathology, Adelaide, SA (Laboratory processes) 
SA Health Communicable Disease Control Branch (co-ordination and IMD surveillance data)  
SAHMRI – whole genome sequencing of N.meningitidis  
Principal Investigator  
Professor Helen Marshall, MBBS MD MPH DCH  
Director, Vaccinology and Immunology Research Trials Unit (VIRTU) 
Deputy Director, Robinson Research Institute, University of Adelaide 
Discipline of Paediatrics 
Women’s and Children’s Hospital 
Email: helen.marshall@adelaide.edu.au  
Co-Investigators 
Associate Professor Ann Koehler BSc MBBS FRCPA MPH 
Director, Communicable Disease Control Branch 
System Performance & Service Delivery, SA Health  
Associate Professor, School of Public Health, University of Adelaide 
Email:  ann.koehler@sa.gov.au  
Mr Andrew Lawrence  
Service Manager 
Microbiology and Infectious Diseases 
Royal Adelaide Hospital  
SA Pathology 
Email: Andrew.Lawrence@sa.gov.au  
Dr Thomas Sullivan 
Statistics Team Leader 
Adelaide Health Technology Assessment 
University of Adelaide 
Email: Thomas.sullivan@adelaide.edu.au 
 
Biostatistician and clinical trialist adviser 
 
Emeritus Professor Philip Ryan 
 
University of Adelaide 
 
South Australia 
Email: philip.ryan@adelaide.edu.au 
 
 

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2  
INTRODUCTION: BACKGROUND INFORMATION AND SCIENTIFIC RATIONALE  
 
2.1 
BACKGROUND INFORMATION  
Adolescents are disproportionally affected by invasive meningococcal disease in SA. in 2016 in SA there were 
27 IMD cases; 4 cases in children < 5 years, 3 in children 5-13 years, 12 cases in adolescents 14-24 years and 9 
cases in adults 25-94 years of age. Over the last 10 years for adolescents aged 15 to 24 years,  the highest 
number of reported IMD cases has been in 18 year olds (Figure 1). This age often coincides with finishing year 
12 and commencing higher education, employment, or travelling. Nasopharyngeal carriage of N. meningitidis 
also has been shown to peak around 18-19 years of age at 24% with a sharp rise in carriage rates from 15 years 
of age  (Figure 2).(5) 
Figure 1: Invasive Meningococcal disease cases in South Australia since 2005 in 15 to 24 year olds. 
 
Figure 2: Meningococcal carriage by age (Systematic review, Christensen et al, Lancet Infectious Diseases)(5) 
 
Pilot Study Part 2:Longitudinal carriage study  

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Data in relation to carriage in Australia are scant and very little is known about overall carriage prevalence of 
Neisseria meningitidis (i.e. all strains), or the proportion of strains that are meningococcal serogroup B. The 
only Australian data available in the literature reporting 1.7% carriage were from a sample of 294 school aged 
children of various ages in Queensland and was conducted in 1989.(12)  The improvement in sensitivity of 
newer molecular diagnostic techniques and the fact that South Australia regularly reports higher Invasive 
Meningococcal Disease rates than Queensland leads us to suspect that baseline carriage in South Australian 
adolescents will be higher than 1.7%. In carriage studies conducted in Europe, carriage prevalence was 
estimated at 4·5% in infants to a peak of 23·7% in 19-year olds. Recently presented carriage rates from 
Nottingham University in the UK ranged from 14.3% - 46.2% for all serogroups at the commencement of the 
university year and 6 months later.[Oldfield N et al. IPNC Mancester, UK, September 2016] Carriage rates for 
serogroup B ranged from 3.3% to 8.5% over the same time period. As no carriage data exist in Australia since 
commencement of the meningococcal C vaccine program, we will conduct a longitudinal pilot study of 500 first 
year university students during orientation week in 2017 at the University of Adelaide (Study Part 2). These 
students will undergo a posterior pharyngeal swab and complete a short questionnaire to collect information 
about possible risk factors at the beginning of university and then 3 months later.  
Age is one the most important factors influencing carriage, with peak carriage occurring around 18- 19 years of 
age. Other factors that influence carriage are being male, concomitant respiratory infections, active and 
passive smoking, number and closeness of social contacts, and low socioeconomic status.(6) Disease is a rare 
outcome of infection (5) but the relationship between carriage and disease incidence is not fully understood. 
With carriage rates significantly higher in adolescents, a reduction in carriage in this group has the potential to 
provide protection to unvaccinated people (herd immunity), including infants.  
Study Part 3: Cross-sectional carriage study 
A carriage study of a cohort of school leavers in SA will provide us with an opportunity to assess carriage rates 
in the population following introduction of an intervention in younger age groups (year 10, 11, 12) and 
compare carriage in individuals who have previously been vaccinated (in years 11 and 12) with individuals who 
are not vaccinated or did not wish to be vaccinated as part of Phase one. We plan to conduct a cross sectional 
carriage study of school leavers (including first year university students) who are at the age group at highest 
risk of invasive meningococcal disease in SA. We will also assess any association between various known risk 
factors and past history of 4CMenB vaccine on prevalence of nasopharyngeal carriage.  
2.2 
RATIONALE  
Study Part 2: This pilot study will establish baseline carriage prevalence in 500 first year university students. 
Very few students will have previously been vaccinated with a MenB vaccine as this study will be conducted 
prior to Phase 1. The findings will assist in validation of study processes for Phase 1, particularly laboratory 
processes. A follow up swab taken 3 months later will provide data on the change in carriage that may occur 
over this 3 month period. Study Part 3 will evaluate carriage rates following introduction of a meningococcal B 
vaccine program, compare carriage rates in vaccinated and unvaccinated individuals and determine risk factors 
for  carriage prevalence  of N. meningitidis genogroups causing disease in South Australian school leavers. 
School leavers are defined as students who were enrolled in year 12 at school in the preceding year of 
recruitment and have been chosen as they are likely to have the highest carriage rates. Following completion 
of Phase 1, a high proportion (approximately two thirds) of students will be immunised by the time of throat 
swab collection in years 2018 and 2019. Assessing carriage in both vaccinated and unvaccinated cohorts will 
further inform the effect the 4CMenB vaccine has on carriage at a population level. This will help inform 
national immunisation program funding of 4CMenB vaccine in adolescents in Australia and internationally.  
 

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2.3 
POTENTIAL RISKS AND BENEFITS  
 
2.3.1 KNOWN POTENTIAL RISKS  
This is an observational study with minimal risks to the participants. Oral pharyngeal swabs may be 
uncomfortable, and may cause a gagging sensation however there are unlikely to be any other effects 
associated with this procedure. 
2.3.2 KNOWN POTENTIAL BENEFITS  
There will be no direct benefits from this study for the participants. Information from this study will assist in 
determining the potential herd immunity effects of meningococcal B vaccines. These data are important to 
inform the cost effectiveness of national and international funded MenB vaccine programs in adolescents. 
3 
OBJECTIVES AND PURPOSE 
 
Pilot Study Part 2: Longitudinal Carriage Study 
Primary Objective  
 
Estimate the carriage prevalence of all genogroups of N. meningitidis in South Australian first year 
university students.  
 
Secondary Objectives 
 
Estimate the carriage prevalence of N. meningitidis genogroups causing disease (A, B, C, W, X, Y) in South 
Australian first year university students. 
 
Identify characteristics associated with carriage prevalence  of all N. meningitidis genogroups in South 
Australian first year university students. 
 
Estimate the change in carriage prevalence of all genogroups of N. meningitidis in South Australian first 
year university students at baseline (first week of university) and 3 months later.  
 
Estimate any difference in  PCR positivity after freezing of the sample at 6, 16 and 48 hours post 
collection. 
 
Estimate any difference in positivity of isolates determined by culture after freezing of samples at 6, 16 
and 48 hours post collection 
Study Part 3: Cross-sectional Carriage Study  
Primary Objective  
 
Estimate the difference in carriage prevalence of disease causing genogroups of N.meningitidis (A, B, C, W, 
X, Y) in South Australian school leavers in 2018 (year 12 in 2017),2019 (year 12 in 2018) and 2020 (year 12 
in 2019)following implementation of a school immunisation program in year 10, 11 and 12 South 
Australian students from 2017-2018. 
Secondary Objectives  
 
Estimate the difference in carriage prevalence of all N. meningitidis genogroups in South Australian school 
leavers in 2018 (year 12 in 2017), 2019 (year 12 in 2018) and 2020 (year 12 in 2019)  following 
implementation of a school immunisation program in year 10, 11 and 12 South Australian students from 
2017-2018. 

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 
Estimate the difference in carriage prevalence of each N. meningitidis genogroup (A, B, C, W, X, Y) in South 
Australian school leavers in 2018 (year 12 in 2017), 2019 (year 12 in 2018) and 2020 (year 12 in 2019)  
following implementation of a school immunisation program in year 10, 11 and 12 South Australian 
students from 2017-2018. 
 
Estimate the difference in carriage prevalence of all N. meningitidis genogroups in South Australian school 
leavers  who have received Bexsero ®  compared to unvaccinated students. 
 
Estimate the difference in carriage prevalence of N. meningitidis genogroups causing disease (A, B, C, W, 
X, Y) in South Australian school leavers  who receivedBexsero ® , compared to unvaccinated students. 
 
Estimate the difference in each N. meningitidis genogroup (A, B, C, W, X, Y) carriage prevalence in South 
Australian school leavers who received Bexsero ®, compared to unvaccinated students. 
 
Identify characteristics associated with carriage prevalence of all N. meningitidis genogroups in South 
Australian school leavers in 2018 / 2019/ 2020 
Identify characteristics associated with carriage prevalence of N. meningitidis genotypes causing disease (A, B, 
C, W, X, Y)  in South Australian school leavers in 2018 /2019 /2020. 
Exploratory objectives 
 
Describe N. meningitidis carriage density for all genogroups in school leavers using qPCR  
 
Describe genome sequencing of pathogenic N. meningitis (A, B, C, W, X, Y) in school leavers. 
4 
STUDY DESIGN AND ENDPOINTS 
 
4.1 
DESCRIPTION OF THE STUDY DESIGN 
Study Part 2: An observational longitudinal study to estimate the carriage prevalence of all genogroups of N. 
meningitidis in South Australian first year university students. This study recruitment will commence during 
orientation week (20th to 24th of February 2017). Students that are enrolled will have a follow up swab taken 3 
months later.  
The student association and university will circulate information about the study to students. This will include 
website coverage and flyers in the orientation week student information packs. A stall will be set up within 
Adelaide University to enroll university students into the study.  The second swab will be taken to coincide 
with timing of vaccination and swabs in the school immunisation program. A private screened section will be 
provided to conduct the throat swabs. A questionnaire will be completed at each visit.  
Study Part 3: An observational cross sectional study to evaluate the impact of 4CMenB vaccination and known 
risk factors on carriage in school leavers. Students previously enrolled in the MenB vaccine herd immunity 
study will also be contacted and offered participation in part 3 of the study to provide an additional swab as 
they become school leavers. The University of Adelaide, University of South Australia, and Flinders University 
will be approached to participate with recruitment of students at each university during orientation week and 
for several weeks after until recruitment has been completed. University health services and involved general 
practices and council immunisation providers may also be involved in collection of swabs for study part 3 . 
Similar to Study Part 2, we will work with the universities and student organisations to disseminate 
information about the study.  
 

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4.2 
STUDY ENDPOINTS 
Primary Endpoints 
Study Part 2:  
Carriage prevalence of all N. meningitidis genogroups as measured by PCR at baseline and 3 months later in 
first year university students. 
Study Part 3: 
Carriage prevalence of N. meningitidis genogroups as measured by PCR in school leavers  
Secondary Endpoints 
Study Part 3: 
Carriage prevalence of all N. meningitidis genogroups as measured by PCR in vaccinated and unvaccinated 
school leavers 
Exploratory Endpoints 
Study Part 3: 
1. Carriage density of N. meningitidis genogroups as measured by qPCR in school leavers in 2018 and 
2019. 
2. Whole genome sequencing of invasive isolates (genogroup A, B, C, W, X, Y) 
 
5 
STUDY ENROLLMENT AND WITHDRAWAL 
 
5.1 
PARTICIPANT INCLUSION CRITERIA 
Individuals eligible to be enrolled into this study are: 
 
South Australian school leavers between 17 to 25 years of age (enrolled in year 12 in the previous 
year ie year 2018, students are eligible if they were enrollled in year 12 in 2017, year 2019, students 
are eligible if they were enrolled in year 12 in 2018 and year 2020, students are eligible if they were 
enrolled in year 12 in 2019 ). 
5.2 
PARTICIPANT EXCLUSION CRITERIA 
 
No exclusion criteria  
5.3 
STRATEGIES FOR RECRUITMENT  
Study Part 2: In 2017, university students from The University of Adelaide will be approached to be involved in 
the study. The sampling frame will occur during orientation week and 500 students will be recruited to provide 
posterior oro-pharyngeal  swabs.  Students will be provided with a $20 iTunes voucher to reimburse their time 
for each visit. 

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Study Part 3: Adelaide’s three largest universities (The University of Adelaide, University of South Australia, 
and Flinders University) will be approached to be involved in the study in 2018 and 2019 and potentially 2020. 
All school leavers aged between 18-25 years will be invited to enrol in the study by use of advertising in the 
university and distribution of postcards and through council immunisation clinics in 2018. Year 12 students in 
Group B who will be returning for 2 doses of Bexsero will be provided with a letter and SMS text message 
reminding them of their vaccinations that are due and the opportunity to further participate with an additional 
throat swab.  At the end of each year a letter will be provided to schools to distribute to all  students in year 12 
to invite their participation for a throat swab the following year. An Enrolled Nurse, Registered Nurse, or 
Medical Officer will collect a posterior pharyngeal swab from all enrolled students. We will be aiming to recruit 
4096school leavers from February – June each year.. The student will be required to fill out a questionnaire 
and provide a one off posterior pharyngeal swab. The survey will collect information  on potential risk factors 
(prior vaccination, smoking history, household size, recent antibiotic use) for the carriage of N. meningitidis. 
No ongoing visits are required. Participants will be offered a $40 voucher to compensate them for travel 
expenses.  
A communications officer will be employed to work with university students union and public relations to 
advertise the study to university students at all 3 universities on establishing appropriate and accessible 
avenues of communication. Involving students in the planning and delivery of communication strategies is 
expected to facilitate two way communication and provide opportunities for students to engage in research.  
 
5.4 
PARTICIPANT WITHDRAWAL OR TERMINATION 
 
5.4.1 REASONS FOR WITHDRAWAL OR TERMINATION 
Participants may withdraw from the study at any time at their request.  
5.5 
PREMATURE TERMINATION OR SUSPENSION OF STUDY 
As per Phase 1  
6 
STUDY PROCEDURES AND SCHEDULE 
 
 
6.1 
STUDY PROCEDURES/EVALUATIONS 
 
6.1.1 STUDY SPECIFIC PROCEDURES  
Pharyngeal swabs will be collected from participants using a standard operating procedure (SOP) to ensure 
consistent and optimal collection and handling of swabs. A swab will be placed at the back of the throat and 
swept across the posterior pharynx and withdrawn.  Laboratory procedures/evaluations are described in Phase 
1. 
Study part 2 will additionally measure any difference in PCR positivity for N. meningitidis following freezing at 6 
hours post collection and 16 and 48 hours post collection. This will assist in validating laboratory procedures 
for the RCT study. Once the sample has been received by SA Pathology each sample will be aliquoted into 
three cryovials and frozen at three different timepoints (6 hours, 16 hours, and 48 hours) following collection 
time.  

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Specimen and laboratory flow diagram for study part 2 
 
 
 
 

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6.2 
STUDY SCHEDULE 
 
6.2.1 COMMUNICATION 
A participant information sheet and consent form will be provided to potential participants describing the 
intent of the study, what is involved, potential risks, potential benefits, and consent process.  
6.2.2 ENROLMENT 
Visit 1 – Month 0, Day 0 (Study Part 2 and study Part 3) 
 
Study staff (EN, RN, or MO) will provide each participant with an information sheet and consent form. 
 
They will obtain written informed consent from each participant.  
 
A questionnaire will be provided that will ask for the following information: 
o 
First name 
o 
Surname 
o 
Gender 
o 
Date of birth 
o 
Year of schooling 
o 
Name of school 
o 
Attendance at university or occupation 
o 
Enrolment in the B Part of it study 
o 
Medicare number 
o 
Prior receipt of 4CMenB vaccine (verification of previous Bexsero ®  administration where 
possible)  
o 
Year and month of 4CMenB vaccination 
o 
Cigarettes smoked/day 
o 
Other smokers at home 
o 
History of meningococcal disease 
o 
Number of pub and club visits in the last week 
o 
Number of kissing contacts 
o 
Number of persons sharing a bedroom 
o 
Recent antibiotic use (none, current, stopped last week, stopped last month) 
o 
Number of people currently residing in their household 
 
Conduct pharyngeal swab collection 
 
Provide voucher to reimburse travel costs  
 
Visit 2 – Month 3, Day 0 (Study Part 2 only) 
 
A questionnaire will be provided as per visit 1 
 
Conduct pharyngeal swab collection 
 
Provide iTunes card  
 
6.3 
LABORATORY PROCEDURES/EVALUATIONS 
 
6.3.1 CLINICAL LABORATORY EVALUATIONS  
Pharyngeal swabs will be collected from all students initially at baseline. A standard operating procedure (SOP) 
will be used to ensure consistent and optimal collection and handling of swabs. Samples will be evaluated for 
the presence of specific meningococcal DNA and if necessary also be used as target for molecular typing assays 
such as multi-locus sequence typing (MLST) and whole genome sequencing (WGS). Any sample with a positive 

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molecular assay will then be cultured using classical bacteriology methodology in order to isolate the Neisseria 
species. These isolates can then be characterised by molecular or other means. All laboratory techniques used 
for molecular testing and further typing are currently in use in the SA Pathology Microbiology and Infectious 
Diseases Laboratories. These laboratories are accredited by NATA/RCPA for routine testing of human and 
biological samples. All protocols are documented and reviewed regularly.  They have been subject to 
appropriate validation according to NATA/NPAAC guidelines. Any new molecular assay e.g. detection of sodC 
gene of N. meningitidis will need to be internally validated before routine use. 
6.3.2 OTHER ASSAYS OR PROCEDURES 
All specimens will be subjected to PCR screening for the presence of specific meningococcal DNA (using PorA 
or sodC gene detection). Further molecular analysis will be used to determine which serogroup has been 
detected (A, B, C, W, X and Y). A range of other molecular tests can be performed on isolates of Neisseria 
species in order to subtype them. This includes serogroup determination, MLST typing, porA and porB typing 
whole genome sequencing and metagenomics.  For isolates identified as N. meningitidis, further typing as 
described above will be performed and isolates stored in glycerol broth at -80 degrees Celsius (oC) for further 
analysis.  
A number of samples, particularly strains known to be associated with invasive disease will also be subjected 
to quantitative polymerase chain reaction (qPCR) in order to determine the density of carriage of 
meningococci.  Appropriate well defined calibrated and validated controls will be used as comparators to 
determine the density of the carriage. 
6.3.3 SPECIMEN PREPARATION, HANDLING, AND STORAGE 
A 2mL skim milk-tryptone-glucose-glycerol (STGG) swab will be used  for both molecular and classical 
bacteriological culture methodologies. A request form with details of the swab will accompany each sample. 
Once the samples reach the laboratory, details will be entered into the Laboratory Information System for 
recording, workup and subsequent reporting. The original samples can be stored at -80oC until processed. 
Once processing is complete, the samples will be retained at -80oC.  All specimens will be subjected to DNA 
extraction using the Roche MagNaPure extraction platform for subsequent molecular testing using routine and 
standard protocols. The remaining fluid will be restored at -80oC in case of a need for further analysis. 
6.3.4 SPECIMEN SHIPMENT 
The STGG swabs are the collection swabs and transport material of choice, since they are suitable for both 
molecular and bacterial culture assays. Once collected, they can be kept cool in styrofoam containers(eskies) 
and transported to the nearest SA Pathology collection centre or delivered to the Frome Road or nRAH 
laboratories directly. Transport of swabs from SA Pathology Collection centres to the central laboratory will be 
kept cool using validated transport methods for biological specimens.  

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7 
ASSESSMENT OF SAFETY 
 
7.1 
REPORTING PROCEDURES 
 
7.1.1 ADVERSE EVENT REPORTING  
Adverse events and Serious Adverse events are not expected from Study Parts 2 & 3. Although we do not 
expect any SAE’s to occur in relation to this study, any that occur will be immediately reported to the Principal 
Investigators and to the relevant Human Research Ethics Committee. In particular, if the study related SAE is 
fatal or life threatening, notification to the Principal Investigator and vaccine manufacturer must be made 
immediately, irrespective of the extent of available event information.  Only SAEs that are assessed as related 
to study participation will be reported to the REC. 
Reporting period 
For each participant, the study related serious adverse event reporting period beings at the time of the 
participant’s informed consent, and continues until study participation is complete. If the study investigators 
become aware of a study related serious adverse event after study completion this will also be reported.  
Causality assessment 
The investigator is required to assess and record the causal relationship.  For all SAEs, sufficient information 
should be obtained by the investigator to determine the causality of each SAE.  The investigator is required to 
follow-up the SAE until the event and/or its sequelae resolve or stabilize at a level acceptable to the 
investigator. 
An investigator’s causality assessment is the determination of whether there exists a reasonable possibility 
that any study processes caused or contributed to an adverse event. 
 
Specific Serious Adverse Events (SAE) reporting requirements are not needed in this as this study is 
non-interventional 
 
Any SAE assessed as related to study participation will be reported to the REC. 
 
The investigators will provide or arrange for prompt diagnosis and medical treatment of any research 
related injury experienced by a study subject. Investigators will also notify the vaccine manufacturer 
of any research related injuries from Study Parts 2 or 3.  
7.2 
SAFETY OVERSIGHT 
Safety oversight will be under the direction of the PI, as for study 1.  
 
8 
CLINICAL MONITORING 
As per Phase 1  
 
 

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9 
STATISTICAL CONSIDERATIONS  
 
9.1 
DESCRIPTION OF STATISTICAL METHODS 
 
9.1.1 GENERAL APPROACH 
Logistic regression with adjustment for confouding will be used to identify factors associated with carriage and 
to compare carriage rates annually and between vaccinated and unvaccinated students. Changes in carriage 
between baseline and 3 months later will be evaluated using logistic regression with generalised estimating 
equations. In all analyses of carriage prevalence, effects will be described using odds ratios with 95% 
confidence intervals. 
 
For comparing the difference in PCR +ve samples after freezing of the sample at 6 hours and 48 hours, we will 
compare paired proportions using a logistic model with generalised estimating equations, and assess 
agreement using a Kappa statistic. 
 
9.1.2  BASELINE DESCRIPTIVE STATISTICS 
Descriptive statistics will report percentages, means with standard deviations, median, and/or range (as 
appropriate) for the following: 
 
Age 
 
Socio-economic Index for Areas (SEIFA) categories. Calculated from suburb data 
 
Categorical outcomes for household size 
 
Categorical outcomes for number people that smoke in each house 
 
Prevalence of N. meningitidis all genogroups carriage 
 
Prevalence of N. meningitidis serogroup B carriage 
 
9.2 
SAMPLE SIZE 
Study Part 2:. Assuming a carriage prevalence of approximately 8%, a sample size of 500 university students 
will allow for estimation of carriage prevalence with a precision of +/- 2.4%, where precision is defined as the 
half-width of a 95% confidence interval. 
Study Part 3:. Assuming the  carriage prevalence of disease causing genogroups of N.meningitidis (A, B, C, W, X, 
Y) in school leavers in 2018 is 8%, a sample size of 4,096 students per year will provide 80% power to detect a 
20% relative reduction in carriage prevalence between 2018 and 2019 (two tailed alpha = 0.05). 
  
10 
QUALITY ASSURANCE AND QUALITY CONTROL 
As per Phase 1.  
 
11 
ETHICS/PROTECTION OF HUMAN SUBJECTS  
 
11.1 
ETHICAL STANDARD  
As per Phase 1  
 

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11.2 
INSTITUTIONAL REVIEW BOARD  
As per Phase 1  
11.3 
INFORMED CONSENT PROCESS  
 
11.3.1 CONSENT/ASSENT AND OTHER INFORMATIONAL DOCUMENTS PROVIDED TO 
PARTICIPANTS 
Consent forms describing study procedures, and risks will be given to the participant and written 
documentation of informed consent is required prior to commencing any study procedures.  
 
11.3.2 CONSENT PROCEDURES AND DOCUMENTATION 
Informed consent is a process that is initiated prior to the individual agreeing to participate in the study and 
continues throughout the individual’s study participation. Consent forms will be HREC approved and the 
participant will be asked to read and review the document. The EN, RN, MO will answer any questions that 
may arise. All participants will receive a written explanation in terms suited to their comprehension of the 
purposes, procedures, and potential risks of the study and of their rights as research participants. Participants 
will have the opportunity to carefully review the written consent form and ask questions by speaking with the 
study staff. The participant will sign the informed consent document prior to any procedures being done for 
the study. The participants may withdraw consent at any time throughout the course of the study. The 
participant will be provided with an copy of the information sheet.  
11.4 
PARTICIPANT AND DATA CONFIDENTIALITY  
Participant confidentiality is strictly held in trust by the participating investigators and SA Pathology. This 
confidentiality is extended to cover testing of biological samples in addition to the clinical information relating 
to participants. Therefore, the study protocol, documentation, data, and all other information generated will 
be held in strict confidence. No information concerning the study or the data will be released to any 
unauthorised third party without prior written approval of the sponsor.  
Study investigators will store identifiable information in locked offices and compactors in the Vaccinology 
Immunology Research Trials Unit (VIRTU) at the Women’s and Children’s Hospital. Electronic data including 
student name, address, and telephone number will be stored on a protected sever at the University of 
Adelaide. 
Study participant research data, which is for purposes of statistical analysis and scientific reporting, will be 
transmitted to and stored at the Women’s and Children’s Hospital. This will not include the participant’s 
contact or identifying information. The study data entry and study management systems used by VIRTU 
research staff will be secured and password protected. At the end of the study, all study databases will be de-
identified and archived at the University of Adelaide. 
This study is not a human genome-wide association study and no human genetic material will be analysed.  
11.4.1 RESEARCH USE OF STORED HUMAN SAMPLES, SPECIMENS OR DATA 
 
Intended use: samples and data collected under this protocol may be used to investigate 
N.meningiditis carriage, density, serotype, genotype, and antigen type. No genetic testing will be 
performed on human material. 

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 
Storage: samples and data will be stored using codes assigned by SA Pathology or the study team. 
Data will be kept in password-protected computers. Only investigators, study staff, and SA Pathology 
staff will have access to the samples and data.  Patient identification data will be entered into the 
secure laboratory information system. Consolidated reports can then be generated from this system. 
All staff who have access to the laboratory information system are bound by the Public Sector rules 
and regulations pertaining to patient and result confidentiality. 
 
Tracking: Data will be tracked using accredited SA Pathology procedures and systems. 
o 
Disposition at the completion of the study: All stored samples will remain in frozen storage at 
SA Pathology and may be used for further testing to assess the N. meningititidis and 
associated microbiota.  
11.5 
FUTURE USE OF STORED SPECIMENS  
After the study is completed, biological samples will be stored at SA Pathology and/or University of Adelaide. 
These samples could be used for research into N.meningiditis genotype and vaccine antigen coverage. Samples 
will be provided with a code-link that will allow linking the biological specimens with the phenotypic data from 
each participant, maintaining the masking of the identity of the participant if they are to be sent to external 
laboratories.  
During the conduct of the study, an individual participant can choose to withdraw consent to have biological 
specimens stored for future research. However, withdrawal of consent with regard to biosample storage will 
not be possible after the study is completed. 
12 
DATA HANDLING AND RECORD KEEPING  
 
12.1 
DATA COLLECTION AND MANAGEMENT RESPONSIBILITIES  
Data collection is the responsibility of the EN, RN, MO, and trial staff at VIRTU. The investigator is responsible 
for ensuring the accuracy, completeness, legibility, and timeliness of the data reported. 
Clinical laboratory data will be entered into existing SA Pathology data systems. These will then be exported 
and combined in a database on the University of Adelaide Server (AHTA).  The data system includes password 
protection and internal quality checks, such as automatic range checks, to identify data that appear 
inconsistent, incomplete, or inaccurate.  
Once matched and the data is cleaned it will be de-identified. The Investigator is responsible for keeping a 
code list so that it is possible to link a participant code to a particular participant. This code list will be kept 
separately on the University of Adelaide server to ensure that in the case of an emergency, a participant can 
be identified.  
12.2 
STUDY RECORDS RETENTION  
As per Phase 1   
13 
STUDY ADMINISTRATION 
 
13.1 
STUDY LEADERSHIP 
As per Phase 1 

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14  
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