Project Neonatal Sepsis (nSEP)
Research type
Research Study
Full title
nSeP: Detecting Neonatal Sepsis by Immune-Metabolic Network Analysis
IRAS ID
248404
Contact name
Peter Ghazal
Contact email
Sponsor organisation
Cardiff University
Clinicaltrials.gov Identifier
Duration of Study in the UK
4 years, 11 months, 31 days
Research summary
Project Neonatal Sepsis\n\nSevere infection or sepsis in newborn babies is a significant global problem, and remains a major cause of morbidity and mortality, especially in preterm and low birth weight babies. Although mortality from neonatal sepsis is low in the UK, it remains difficult to diagnose using traditional clinical signs or blood culture tests. Thus, a combination of risk factors suggesting sepsis and non-specific clinical signs are used to start treatment with antibiotics in babies, leading to overuse of antibiotics.\n\nStudies have shown that the human gene responds to infection even before the onset of symptoms by producing extensive networks of inflammatory molecules. We have shown that systematic measurement and detection of these molecules in blood from 52-genes and their networks can achieve >99% accuracy for detecting bacterial infection with 100% sensitivity, showing superior performance to previously characterised markers. This was true even in babies with blood-culture negative results, illustrating the specific diagnostic benefits of the particular combinations of markers. \n\nThe unexpectedly high accuracy and sensitivity values could not have resulted from the investigation of any of the individual markers alone, nor could they have been predicted. These studies provide a proof of concept but need independent confirmatory studies as well as investigating specificity against non-bacterial (viral and fungal) infections and non-infective inflammation. \n\nWe hypothesise that analytical measurement of networks of immune and metabolic pathways that selectively change upon infection can be an ideal screening test for neonatal sepsis, and for discriminating against viral infection. We plan to collect blood samples from babies with suspected sepsis (cases) and compare them against babies without any infection (controls). The study will be conducted over several sites in the UK, over a period of 3-5 years. [COVI-19 Amendment 18/05/2020] This substantial amendment refers to our request for the inclusion of infants specifically suspected to have COVID-19 infection. In the current pandemic we will focus on these cases alone, as it is extremely important to study the\nimmune response in those patients if we are to understand more about disease severity, and how to manage it in the\ncontext of sepsis. We will test the specific hypothesis that severe cases will develop a measurable systemic\nresponse. If a systemic response is detected then this will be investigated against the bacterial sepsis biomarkers and further tested for any underlying possible viral associated sepsis response. This may lead to the development of rapid tests, novel treatments and to a better understanding of COVID-19 pathology and epidemiology in comparison with other infections. This group of infants will get separated into two sub-groups: confirmed COVID-19 cases or negative controls. The suspected but not confirmed cases will further comprise of those patients that may subsequently develop bacterial/fungal sepsis or viral sepsis that is not COVID19 or are not infected. Due to the\ncurrent pandemic situation and change in working practices within clinical areas, we propose to temporarily collect\nsamples for COVID-19 suspected patients only. Recruiting the full range of cases and controls will resume once working patterns return to normal after the pandemic. We wish to temporally change the current consent process to allow telephone consent of parents/ guardians while there are visitor restrictions in the NICU due to Covid outbreak, if verbal consent is given samples will be stored and will only be used and analysed for the study once written\nconsent is obtained, we plan to get written consent at the earliest opportunity i.e. when parents allowed back into the\nNICU.\nWe also propose to include an additional laboratory technique called RNAseq as part of the pathway network analysis on whole blood and the linking of the nSEP study with mSEP study (IRAS Ref: 262062) on the condition that mSEP receives all the approvals to proceed with recruitment. This additional method offers several key advantages over current hybridisation methods, such as microarrays. These advantages include a greater sensitivity for quantifying gene expression that enables investigation of genes not specified on microarrays, such as viral encoding transcripts, and detecting more statistically significant genes as a result of much lower background noise, in comparison to microarrays. Further advantages include the ability to detect precise genetic information that allows, for example, examining the antibody and T-cell repertoires of the immune system as well as detecting sequence variants in the exons of genes. Thus, RNAseq will allow us to interrogate known biomarker targets while exploring new ones and provide a deeper analysis of the host immune response to infection. For further information on the RNAseq please see information in link\nhttps://cofactorgenomics.com/advantages-rna-seq-over-microarray-t echnology/RNAseq has improved and become more robust utilises the most advanced next-generation sequencing methods to\nprovide a quantitative approach to profile the complete set of genes. However, this method generates raw data that can potentially be used to identify genetic differences and therefore could be classed as genetic material. RNAseq only determines the genetic content of a small fraction of the entire human genome – approximately 1%. This 1% will contain some genetic information unique to the individual. So, like a fingerprint, if this 1% were to be sequenced again for any other purpose, it may be possible to statistically link 2 anonymised datasets. Although, it is notable that\ngene expression levels vary over time making this exact matching highly improbable. For our current project, this means we shall use this method to investigate changes in gene expression levels of our known biomarkers. Further, we will be able to explore new potential gene expression markers important in sepsis as well as including in future analysis of immune gene recombination events (detailing the immune repertoire, and any immune genetic coding\nvariants). A requirement of publication of the results generated from this type of data would require us to upload the anonymised raw sequence data onto a database with controlled access, for use by other researchers. The raw data mentioned are in two forms: 1 FASTQ file containing the genetic information about the above mentioned 1% of the\ngenome, this information is the actual genetic sequence of those genes which are active i.e. expressed in the individual as part of the study. 2. Counts files, these contain no genetic information and are derived from the FASTQ files and contain the level of expression of each gene in the individual. When publishing we will use a public repository for the gene expression levels (e.g GEO or ArrayExpress) and the genetic information we will use a database with controlled access, one option being dbGaP and SRA (https://www.ncbi.nlm.nih.gov/sra/docs/submit/).\nThis means we can give researchers free access to the counts’ files containing no genetic information but control access to the FASTQ files with genetic information. The controlled access will be managed by a data guardian, who will be the study PI. A researcher would be required to make an application to access this controlled data before\naccess is granted or denied. The PI will review with the CI applications and grant access on a case by cases basis based on the potential merits of the external researcher’s proposal. This process is managed through the public repository, this approach is used commonly for studies of this type. As such we wish to update all relevant study documents to reflect this to ensure participants can make an informed choice on whether to take part in the study. We are not altering the experimental plan, scientific objectives, only the method used to measure the changes in the transcriptome (gene expression levels). Conditional Linking nSEP and mSEP Studies (IRAS Ref:262062) In the womb, baby and Mum’s immune systems are in close communication and upon infection of Mum she will alert the babies immune system causing an inflammatory reaction in baby --- we wish to link a septic Mum’s response with the baby’s immune response testing the hypothesis that a non infected baby will reflect the alerted immune response of septic or COVID19 positive mum. Therefore, we wish to link health data and outcomes between our Mother and Baby pairs, this would be on condition of the mSEP receiving approval. Any woman who has been recruited into the maternal sepsis cohort B (developed sepsis) during labour or delivery, and have been put onto the sepsis pathway will be approached to link research records with their babies. Current routine practice is for the maternity team to inform the neonatal team of mother’s sepsis diagnosis. The neonatal team monitors the baby and assesses probability of infection by using a sepsis risk calculator tool, placing the baby on antibiotics if necessary. Therefore, this gives us a good opportunity to utilise normal practice within the teams for mother and baby to be linked if mothers have been consented for their baby to participate in nSEP study. The research midwife and research nurse from the respective teams will be the main points of contact and for maintaining the records In order to fulfil the data linkage element of the study (whereby information about the mother’s health are obtained\nfrom the mother’s medical records), only the baby’s biological mother will be able to agree to the following statement on the consent form: ‘I give permission for researchers to access the baby’s mother’s medical notes, including the hospitals electronic records, to obtain information relevant to the study as detailed in the information sheet. This information will be obtained, anonymised and held in a secure format.’ If the mother is not available to complete this section of the consent form, then this statement will be left blank and the mother’s records will not be accessed for the purposes of the nSeP study.
REC name
Wales REC 2
REC reference
19/WA/0008
Date of REC Opinion
3 Apr 2019
REC opinion
Further Information Favourable Opinion