Microbiology, Virology and Infection Control

Translational Research in Molecular Microbiology

Investigating the role of infection in pre-term labour

Broad-range 16S rDNA PCR and other real-time PCR assays for specific bacterial targets have been developed in the Clinical Microbiology laboratory at GOSH [1] and are now used in routine diagnostics. These techniques have been used in this study to investigate the role of bacteria in pre-term labour by detecting bacterial DNA in placental samples. Initial findings indicated a differing prevalence in bacterial DNA in pre-term and term labours [2]. The project continues, using deep sequencing techniques to further study the microbiome of placental tissue in pre-term and term labour.
This  research is funded by SPARKS and is a collaboration between Microbiology Department (GOSH), Infectious diseases and Microbiology (ICH) and the Obstetrics and Gynaecology department (UCLH).

Reducing hospital acquired infections due to gram negative organisms

This project aims to control the spread of MDR gram negative bacteria by focusing on rapid diagnostic techniques, improving control mechanisms by examining isolation policies and finally identifying factors that lead to poor clinical outcome when colonisation occurs. The research is  funded by NIHR (5 year Healthcare Scientist Research fellowship)

Identification and typing of M. abscessus complex strains isolated from the lungs of Cystic Fibrosis (CF) patients and association with clinical outcomes

Identification of non-tuberculous Mycobacteria (NTM), in particular M. abscessus complex strains, has proved problematic. We have developed a new sequencing based identification method and this has led to us beginning to investigate the role of particular M. abscessus strains on clinical outcome. We initially used a commercially available rep-PCR typing assay called Diversilab and have recently collaborated with a laboratory at the HPA Centre for Infections to develop a VNTR (Variable Number Tandem Repeat) typing scheme for M. abscessus. Preliminary data suggests that there are two strains of M. abscessus that are associated with persistent colonisation in CF patients. This data will be presented as a poster at the European Society by obtaining whole genome sequences of a selection of clinical M. abscessus isolates.

Collaborative research projects

Broad-range 16S rDNA PCR and other molecular methods developed in the Clinical Microbiology Laboratory are a key part of a number of other research studies based in the Infectious Diseases and Microbiology department at ICH, including:
• Broad-Range 16S rDNA PCR in children with HIV on Antiretroviral Therapy
• Investigating microbial translocation in children with HIV in Uganda using molecular diagnostics
• Molecular diagnosis of neonatal sepsis in Uganda
• Investigating microbial translocation in surgical infants requiring parenteral nutrition at GOSH.


1. Harris KA and Hartley JC (2003). Development of broad-range 16S rDNA PCR for use in the routine diagnostic clinical microbiology service.J Med Microbiol.52(Pt 8):685-91.

2. Jones H, Harris K, Azizia M, Bank L, Carpenter B, Hartley J, Klein N and Peebles D (2009). Differing prevalence and diversity of bacterial species in fetal membranes from very preterm and term labour. PLoS ONE. 4 (12): e8205.

3. Kathryn Harris, Dervla Kenna, Cornelis Blauwendraat, John Hartley, Jane Turton and Garth Dixon. Molecular Fingerprinting of the Mycobacterium abscessus complex. 29th Annual meeting of the European Society for Paediatric Infectious Diseases (ESPID). The Hague, the Netherlands June 7-11, 2011.

Using lipo-oligosaccharide modification to generate a novel vaccine to protect against serogroup B meningococcal disease.

Primary Investigator Garth Dixon - Co-applicants Dr Jeremy Brown UCLH and Dr Peter van der Ley, National Vaccine Institute of Netherlands, Bilthoven.

Although more basic science this is a proof of principle project to improve current meningococcal vaccines via genetic modification of bacterial LPS. This results in a candidate vaccine that is targeted for uptake by human Dendritic cells, induces their maturation and ensures that cross protective lipoproteins are retained in the vaccine preparations. We hope by the end of project that there is sufficient data to justify a first in man study.

Output so far -
• Using lipooligosaccharide modification to generate a novel vaccine to protect against serogroup B meningococcal disease. Jones, HE, Hamstra, H, Brown, J, Klein, N, van der Ley, P and Dixon, G. Oral presentation 17th International Pathogenic Neisseria Conference (2010, Banff, Canada).
• Jones, HE, Klein, N and Dixon, G. Human dendritic cell culture and infection. Methods in Molecular Biology. Methods Mol Biol. 2012;799:217-35.
• Two papers in preparation

Collaborative Translational Research

Early detection of lung disease in infants with Cystic Fibrosis (CF) diagnosed by newborn screening using objective, standardised measures of infection, inflammation, lung structure and function

Funded by: The Cystic Fibrosis Trust and GOSH Special Trustees

Other Research Projects - James Soothill

 Use of phage in the control of multiply-antibiotic resistant Enterobacteriaceae

Enterobacteriaceae resistant to antibiotics pose a serious threat to the management of neutropenic hospital patients. No new classes of agents that can be used against them in younger children have been developed for over 30 years. The pharmaceutical industry is reducing investment in the development of anti-infectives at a time when the worldwide spread of carbapenemase determinants threatens the usefulness of the newest and broadest agents. Phages have been shown to control gut populations of Enterobacteriaceae in farm animals so might be an effective control of the antibiotic resistant strains of Enterobacteriaceae found in hospital patients. Reducing intestinal counts of such bacteria might limit cross infection and also prevent spread. We are isolating new phages for Kebiella spp and Enterobacter spp, assessing their efficacy against antibiotic-resistant hospital strains and will shortly be evaluating their effects on gut flora in mice. This work could lead ultimately to new ways of preventing infections by such bacteria.

Investigation of the role of Lactobacillus phages in the development of bacterial vaginosis

The first abnormality seen in bacterial vaginosis (BV) is a loss of lactobacilli in the vaginal flora. This might be due to an infection of the lactobacilli by bacteriophage. We have been and intend to continue studying vaginal swabs from patients with BV to see if phages are present.

Pilot study of the use of nebulised autologous serum in the treatment of CF patients with P aeruginosa infection

The P aeruginosa strains of CF patients are very sensitive to the serum of the patients from whom they were derived and yet they persist in the patient's lungs. One reason for this might be that the serum substances do not gain sufficient access to the P aeruginosa strains. We (Paul Aurora and I) will obtain serum samples for CF patients and administer them by nebuliser to the patients and look for any beneficial or adverse effects. This work may lead to a full scale clinical trial in this debilitating and ultimately fatal infection.


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