The genetic basis of meningococcal and other life threatening bacterial infections of childhood

Bacterial infection is the major cause of disability and death in children
worldwide. We will use meningococcal
disease (MD) as a model to understand genetic factors underlying susceptibility
and severity of childhood
bacterial infection. In addition to MD, we will study infections caused by the
following four bacterial pathogens often causing severe disease: pneumococci,
Staphylococcus aureus, Group A Streptococcus, and Salmonella species. We have
already undertaken a genome wide study (GWAS) to identify genes causing
susceptibility to meningococcal disease in a European cohorts. In this study we
identified complement factor H (fH) and fH-related (fHr) genes controlling MD
susceptibility. (Davila et al Nature Genetics 2010;42 (9) 772-6) In addition we
foundSNP's in other genomic regions in other pathways which may also control
susceptibility for MD.
Based on this study Professor Levin form Imperial College London together with
researchers from Spain, Austria, and The Netherlands, who were involved in the
previous study an interdisciplinary multinational team was formed including
experts on paediatric infectious diseases, but also experts on immunogenetics,
bioinformatics, molecular microbiology, vaccinology, and Research and
Development in the area of diagnostics development, vaccine development, and
genome analysis.
Currently materials available within the consortium (±2800 DNA samples of
children with MD and ± 3500 DNA samples of children vaccinated with an
experimental vaccine against meningococcal serogroup C or B ) are analysed in
the Genome Institute in Singapore to identify genetic factors that control
severity of disease.
The previous finding related to factor H (fH) and fH-related (fHr) genes
controlling MD susceptibility is fundamental to prevention as novel vaccines
containing the MD fH receptor protein as a component are undergoing trials.
In the here presented study we will use next generation sequencing to identify
the causal variants within the fH/fHr region and other regions and pathways
that control susceptibility and severity of meningococcal disease,
pneumococcal disease, staphylococcal disease, Group A Streptococcal disease and
Salmonella species disease. We will match bacterial and host genetic
variation.
Here to we will apply next generation sequencing, RNA expression analysis,
functional analyses and animal models. We expect to identify Mendelian defects
and rare mutations as well as copy number variation and epi-genetic effects.
The study will contribute to the identification of mechanisms underlying
susceptibility, and may provide new targets for treatment and prevention.

The main objective of this part of the study (Work Package 1, WP1) which is
part of a n European Union funded FP7 project entitled EUCLIDS is to develop,
maintain and regulate the clinical network required to collect clinical data
and patient material ( DNA, blood, urine) to form a biobank.
The meningococcal disease consortium with partners from the United Kingdom,
Spain, Austria and The Netherlands already holds the most important
meningococcal disease (MD) biobank in the world, with more than 2,800 DNA
samples and clinical records of children with MD; 2,500 of these samples have
already been genotyped. Four thousand new patients will be recruited with the
inclusion criteria - patients
0 to 18 years old, presenting with a severe bacterial infection (defined as
suspected infection plus systemic
inflammatory response syndrome, as per internationally agreed definitions,
and/or clinical syndromes suggesting
invasive infection with meningococcus, pneumococcus, staphylococcus (Europe &
West Africa) or salmonella
(West African cohort only).
The EUCLIDS international clinical network constitutes a key component of the
project as a whole and is
fundamental to all the work packages and partners. The clinical network will
provide all necessary patient
cohorts for all other work packages, including GWAS, fine mapping, sequencing,
replication or validation studies.
Prospective *extreme phenotype* cohorts which will be selected from patients
recruited in the intensive care units will be phenotyped using internationally
defined criteria of severity and organ failure. In this smaller group of
patients blood samples (RNA, DNA and serum) will be taken at t=0, t=24 and
t=72 hour and stored using defined sample handling methods for later use in
*Beyond State-of-the-Art* genomic studies.
The consortium partner Micropathology Ltd (MIC) will provide *Beyond
State-of-the-Art* molecular diagnostics to increase the pathogen detection rate
in culture negative cases of severe infection.
Specifically, the objectives are:
1. To maintain and conduct the international clinical network including
European and African partners.
2. To create the network web-based database.
3. To organize recruitment of patients with specified severe bacterial
infections across all sites.
4. To provide the necessary new patient cohorts for validation of the results
of the different work packages in a
timely manner.
5. To organize and administer the consortium biobank.
6. To regulate, collect and record all the clinical data to be obtained in
order to describe accurate clinical
phenotypes and categorise patients by severity, organ failure and outcome.

We will prospectively recruit paediatric cohorts with meningococcal,
pneumococcal, staphylococcal and group A streptococcal infections during the
first 3 years of the project.

Patients aged 1 month-18 years with invasive infections (meningitis, sepsis,
pleuralempyema, arthritis/osteomyelitis ) caused by meningococci, pneumococci,
Staphylococcus aureus and group A Streptococci may be included.

The Dutch clinical network for the EUCLIDS Project is named Pediatric Dutch
Bacterial Infection Genetics network (PeD-BIG; Coordinator Prof Dr. R. de
Groot). The network is coordinated by the Radboud University Nijmegen Medical
Centre (RUNMC) Prof dr Ronald de Groot and Michiel van der Flier, in
collaboration with Marceline van Furth, (VU-MC Amsterdam). In this study
distinction is made between patients not admitted to pediatric intensive care
units(Category 1) . Inclusion of patients with life threatening infection
(Category 2) admitted to Paediatric Intensive Care Unit will be coordinated by
Erasmus University Medical Center Rotterdam (EMC; Jan Hazelzet / Marieke
Emonts).

Patient recruitment to take place over 36 months with 3 months' lead in time
for staff recruitment and training and 3 months* lead out time for patient
follow up and completion of databases.

Clinical characteristics will be recorded on a web-based clinical report form
for all patients included in the study. Data collected from the medical records
will include complaints at presentation, course of disease, data on the
infecting organisms and severity of illness scoring as well as disease
phenotype and outcomes.

Patients will not need additional vena punctures, as blood sample collection
will be combined with routine blood sampling.
In non-PICU patients there will be 1 blood sample with a maximum volume of 8 mL
In PICU patients there will be 3 sequential blood samples each with a maximum
volume of 8 mL at t=0, t=24 hours and t=72 hours. In addition, on admission an
urine sample and nose swab will be collected.
In young infants < 12 months volume for each sample will be reduced to maximum
volume of 4 mL.
In patients retrospectively recruited for the study saliva will be collected
for DNA isolation. In these patients no blood sampling will occur.

DNA analysis will be performed anonimized. The participants will not be
informed on their own genetic code (DNA). Thus the DNA analysis will not have
juridical impact (when gaining a mortgage or life insurance)

Bacterial isolates will be stored by the Netherlands Reference Laboratory for
Bacterial Meningitis and in time transported to the relevant workpackage. Blood
and urine samples and nose swabs will be processed and stored at the site and
then batched and transferred to the laboratory performing the relevant work
package including genome wide association study (GWAS), next generation
sequencing, RNA expression analysis, "Beyond-State-Of-The-Art" Genome studies,
and advanced molecular diagnostics.

No risks.
No individual benefit.
The group relatedness is clear since the risk on a severe course of a bacterial
infection in a child is much greater than in adults. This is caused by a
combination of a -still- immature immunesystem and genetic factors influencing
the immunity. In adults other factors such as secondary immunodeficiency are
more frequent. An example is alcoholism or chronic disease as a risk factor for
pneumococcal infections. life threatening bacterial infections in childhood
remain an important cause of morbidity and mortality despite current
availability of antibiotics and vaccines. A better understanding of genetic
determinants may provide new leads to improve therapy and prevention and to
identify risk groups for increased susceptibility and unfavourable outcome.