Infectious Diseases & Microbiology

The research of the Infectious Diseases Group focuses on improving the diagnosis, treatment and prevention of infectious diseases in children. It comprises both clinical and laboratory-based research studies. The clinical research aspect includes randomised controlled trials, observational studies and systematic reviews of best practice. Our laboratory research encompasses basic and applied medical microbiology, as well as immunological studies to explore the mechanisms by which pathogens cause disease and their interaction with the host immune response.

We have a particular interest in infections that are important to child health worldwide such as tuberculosis and other respiratory infections, diarrhoeal illnesses and neonatal sepsis. A key focus of our current work is the investigation of the heterologous effects of BCG vaccination. The team are investigating the hypothesis that the immunomodulatory effects of BCG influence the development of infant immunity to enhance protection against infections and reduce susceptibility to allergic disease.

MIS BAIR - BCG for allergy and infection reduction study

Group Leaders: 
Kaya Gardiner
Role: 
Group Research Coordinator
Susie Germano
Role: 
Senior research assistant
Frances Oppedisano
Role: 
Senior research assistant
Snezana Spillane
Role: 
Research assistant
Rhian bonnici
Role: 
Research assistant
Benjamin Forbes
Role: 
Research assistant
Dr Vanessa Clifford
Role: 
PhD Student
Dr Bridget Freyne
Role: 
PhD Student
Dr Josh Wolf
Role: 
PhD Student
Dr Lianne Cox
Role: 
PhD Student
Dr Amanda Gwee
Role: 
PhD Student
Freya Summons
Role: 
PhD Student
Veronica Abruzzo
Role: 
Data Manager
Clare Morrison
Role: 
Research coordinator (MIS BAIR)
Liz Perkins
Role: 
Research coordinator (VANC study)
Monica Owlad
Role: 
Research Nurse
Julie-Ann Quinn
Role: 
Research Nurse
Judith Spotswood
Role: 
Research Nurse
Kate Wall
Role: 
Research Nurse
Dr Tom Connell
Role: 
Research Officer
Dr Eva Sudbury
Role: 
Research Officer
Dr Joshua Osowicki
Role: 
Research Doctor
Dr Bernadette Cranswick
Role: 
Research Doctor
Dr Nicole Messina
Role: 
Research Officer
Rhian Bonnici
Role: 
Research assistant
Dr Freya Harewood
Role: 
PhD Student
Dr Samantha Bannister
Role: 
PhD Student
Dr Petra Zimmermann
Role: 
PhD Student
Gill Ormond
Role: 
Research coordinator (MIS BAIR)
Hannah Elborough
Role: 
Research Nurse
Casey Goodall
Role: 
Study Assistant
Victoria Scott
Role: 
Study Assistant
Simone Hamilton
Role: 
Research Nurse

Clinical infectious diseases

Research is conducted in close collaboration with the clinical infections diseases team at The Royal Children’s Hospital. We have a large number of ongoing projects on a wide range of topics including the following.

Current studies

  • VANC trial: RCT of continuous versus intermittent dosing of vancomycin in neonates
  • Antibiotic penetration of CSF
  • Staphylococcus aureus bacteraemia in children
  • Candida study
  • Stethocloud project

 

Heterologous effects of vaccines

Bacillus Calmette–Guérin (BCG) vaccine is given to over 120 of the 130 million babies born worldwide each year with the aim of providing protection against tuberculosis (TB). It is becoming clear that neonatal BCG vaccination has an additional substantial effect on all-cause infant mortality in high-mortality settings by providing ‘heterologous’ or ‘non-specific’ protection against other infections. It is believed this results from the well-established powerful immunomodulatory effects of BCG that have been demonstrated both in vitro and in vivo. These effects and the ability of BCG to train the developing immune system may also lead to reduced susceptibility to allergic disease.

Understanding how BCG vaccination enhances the developing immune system is important because:

  • Harnessing the beneficial immunomodulatory effects of BCG could significantly reduce neonatal and infant morbidity and mortality worldwide.

Understanding the beneficial non-TB-related effects of BCG is critical for global BCG vaccine policy and the development of new TB vaccines

  • Changes in BCG vaccine policy may result in the loss of the beneficial heterologous effects of BCG with a consequent detrimental effect on morbidity and mortality. This includes:
    • replacing BCG with a more specific vaccine in high TB prevalence countries
    • removing BCG from the standard schedule in emerging economies with diminishing rates of TB.
  • A better understanding of BCG’s heterologous effects will remain relevant in the era of novel TB vaccines as many of the vaccines in development are designed to boost a birth dose of BCG vaccine.

Current studies:

The MIS BAIR randomised controlled trial
The Melbourne Infant Study: BCG for Allergy and Infection Reduction (MIS BAIR) is an Australian NHMRC-funded randomised controlled trial (RCT) that will assess the effect of neonatal BCG vaccination on clinical allergy and infection outcomes in infants in Melbourne. Over 1400 infants are being randomised to BCG or no BCG at birth. Infants will be followed up for one-year using three monthly online questionnaires to collect data from parents on allergic, infection and other outcomes. At one year of age, all infants will undergo testing to determine the prevalence of allergy to food and other allergens. The study also includes the collection of blood and other biosamples, providing a unique opportunity to rigorously test the hypothesis that neonatal BCG vaccination has lasting heterologous effects on infant immunity.

There has been a dramatic rise in allergic disease worldwide since the 1980s. Asthma rates increased first, followed by eczema, allergic rhinitis and, more recently, food allergy - especially in infants and young children. In Australia, the prevalence of allergic disease is particularly high: up to 30% of children are affected, and eczema and asthma are among the most common chronic diseases of childhood. Preventing allergic disease by an immunomodulatory intervention early in life would be a major advance with significant implications for individual health and public health resources. BCG vaccination is a potential intervention with an established safety profile. The heterologous effects of BCG on innate immunity and the cellular immune response could prime host immunity away from an allergic pathway. Observational data and one small RCT suggest that BCG vaccination at birth leads to a substantial reduction in allergic disease - however, there is an absence of level 1 evidence.

Clinical outcomes
The aim of this study is to determine the influence of BCG at birth on infant immunity and the development of allergy by comparing infants given BCG at birth with those not given BCG to determine if BCG vaccination leads to a reduction in the following measures of allergy in the first 12 months of life:

Primary:

  • Food sensitisation (skin prick test)
  • Eczema
  • Lower respiratory tract infection (LRTI)

Secondary:

  • Challenge-proven food allergy
  • Hospital admissions for respiratory illnesses.

Immunological outcomes
Data are emerging to account for BCG’s heterologous effects, including studies that show BCG modulates innate immunity through epigenetic reprogramming of monocytes. However, this has never been explored in the context of neonatal BCG vaccination, the main target population for BCG use worldwide.
A recent JAMA editorial lamented the absence of “prospective studies designed to explore the immunological mechanisms underlying the apparent reduction in infection syndromes not targeted by the administered vaccine”. Our unique cohort of BCG vaccinated and BCG naïve infants who are being followed up longitudinally from birth in the MIS BAIR study provides us with the unparalleled opportunity to investigate the immunological and molecular mechanisms whereby BCG mediates beneficial heterologous protective immunity.

To this end, in addition to the clinical allergy and infection outcomes, we are collecting a large number of biosamples, for immunological and studies.  These include the following:

  • cord blood
  • venous blood at seven days, six months and one year of age
  • stool samples daily for the first seven days of life for microbiome analyses
  • respiratory samples for viral and microbiome analyses. 

The BabyBAIR study
In this observational study we are investigating how BCG vaccination modifies the immune response to subsequent (in vitro) challenge with viral and bacterial pathogens unrelated to TB in healthy children and young adults.

ELVIS (Early Life Vaccine Immunity Study)
This is a randomised controlled trial to determine the heterologous effects of BCG and Hepatitis B vaccination at birth on neonatal immune responses. It is designed to investigate the possible interaction between these two vaccines on the innate and adaptive immune response in the first 7 days of life.
The study will include 200 newborn babies who require BCG vaccination. They will be randomised to one of four groups shortly after birth, which will determine which birth dose vaccines they will receive:

  • Group 1 BCG vaccine
  • Group 2 BCG vaccine and Hepatitis B vaccine
  • Group 3 Hepatitis B vaccine at birth
  • Group 4 No birth vaccines

Seven days post-randomisation they will have venous blood collected for analysis and subsequently receive any vaccines they still require. In addition to this blood sample, stool samples will be collected daily for the first seven days of life and nose swabs will be collected at randomisation and the seven-day visit for microbiome analysis.

Childhood tuberculosis

There are approximately 1.3 million new cases of active TB every year in individuals under 15 years of age worldwide, and TB claims the lives of over half a million children annually. The prevalence of TB is increasing worldwide and XDR-TB now poses an additional threat. One third of the world’s population is infected with TB and there are nine million new cases of active TB disease every year. Recent data show that children account for an increasing proportion of cases of TB in both developed and developing countries  and the disease remains a major cause of morbidity and mortality in children worldwide.
The research and development targets of WHO’s Global Plan to Stop TB include the need for new diagnostics, new drugs and new vaccines. Our TB research focuses on creating new techniques for the diagnosis of childhood TB, and understanding the immune response and adverse events of BCG (the current TB vaccine). We are have a number of clinical and epidemiological projects.

Biomarkers for immunodiagnosis and monitoring of TB
We were amongst the first researchers to investigate the performance of interferon-gamma release assays (IGRA) in children. Our studies highlight that compared to adults, in children there is a substantially higher rate of discordance with the tuberculin skin test (TST) – suggesting diminished sensitivity – and a higher rate of indeterminate assays. The findings, subsequently confirmed by other groups worldwide, have important implications for the diagnosis and clinical management of children with suspected TB.

We have subsequently used detailed immunological analyses (using whole blood assays with TB-specific peptides and multi-colour flow cytometry and bead-based multiplex (Luminex XMAP) cytokine assays) to search for more accurate biomarkers for the diagnosis of TB in children.
As a result of our work over the last seven years, we have identified novel characteristic Mycobacterium tuberculosis (MTB)-specific cytokine responses (biomarkers) in blood that have the potential to improve the immune-based diagnosis of TB and, critically, simultaneously to distinguish between LTBI and active TB.
Our current studies assess the validity of these biomarkers, TST and IGRA in adults and children in a low TB prevalence setting and children in a high TB prevalence setting (Peru project).

Current studies

IDOCT (Immuno-Diagnosis of Childhood Tuberculosis)
This NHMRC funded study recruited 149 children and found a number of novel cytokine responses that can distinguish between TB-uninfected and TB-infected children. In addition, some of these cytokines have the ability to distinguish between latent TB infection and active TB.
Further participants are currently being recruited to validate these findings in children in Melbourne children. Also, the TB biomarkers identified in this project are currently undergoing further investigation in two further studies (VIDA and the Peru project) in adults and children. These studies will assess the performance of the biomarkers in different age-groups and settings (low and high TB prevalence), a key step in the development of a novel TB test for clinical use. 

VIDA (Validation of ImmunoDiagnostic markers in Adults)
In this study we are further evaluating and validationg the novel biomarkers discovered in the IDOCT study in a Melbourne adult population. This validation study will establish the performance of the biomarkers in adults, a key step in the development of a novel TB test with sufficiently high sensitivity and specificity for use in the clinical setting.

Peru childhood TB diagnosis project
In collaboration with our colleagues in Lima, Peru, we are testing novel biomarkers in children in a high TB prevalence setting to determine their precise sensitivity and specificity. This validation is a critical step in the development of a new generation of low cost, point-of-care immunodiagnostic assays for TB. In this prospective cohort study, we are enrolling 200 children aged 0-14 years who are household contacts of adult TB patients and thus at high risk of latent TB infection or TB disease.

Immune response to BCG

We have undertaken a number of studies investigating the immune response to BCG immunisation, and in particular the influence of vaccine strain and age of administration (birth vs 2 months, and child vs adult). These studies have used short and long term whole blood assays with a variety of mycobacterial antigens followed by analysis using multi-colour flow cytometry and bead-based multiplex (xMAP Luminex) cytokine assays. We have published a number of studies describing the role of polyfunctional T cells and CD107-expressing T cells in the immune response to BCG vaccination. A paper currently under review reports the result of our recent study that highlights the importance of NK cells and CD4-CD8- ‘double negative’ T cells in the immune response to BCG.

Current studies:

  • Further studies will be undertaken as part of the MIS BAIR and BabyBAIR studies
  • Systematic review of adverse effects of BCG

Epidemiology of childhood TB in Victoria

Current studies:

  • Epidemiology of active TB in Victoria
  • Study of the management of child contacts of adults with TB in Victoria

E. coli diarrhoeal disease research

Current studies:

Understanding how Escherichia coli causes diarrhoea
We are studying E. coli to discover how certain types are able to cause diarrhoea and other diseases. The aim of this research is to develop tools that will allow us to distinguish pathogenic from harmless E. coli varieties and to develop interventions to treat and prevent infections with these bacteria.

Prevention of infections with enterotoxigenic Escherichia coli
Enterotoxin-producing strains of E. coli are an important cause of diarrhoea and death in children in developing countries, and the commonest cause of travellers' diarrhoea worldwide. As no effective vaccines are available for these infections, we are investigating a novel technique for vaccine delivery to develop one. We are also working on strategies to prevent travellers' diarrhoea that do not require immunisation.

Collaborations: 
  • Centre of Research Excellence on Tuberculosis Control: From Discovery to Public Health Practice and Policy
  • Prof Tobi Kollman, Director of Flow Cytometry Facility, Child & Family Research Institute; Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia (UBC) and British Columbia's Children's Hospital, Vancouver, Canada.
  • Prof Mihai Netea, Professor of Experimental Medicine, Department of Internal Medicine, Radboud University Nijmegen Medical Centre, The Netherlands