CIDMPH Research Activities
Research programs are being conducted in the following areas;
- Bacterial Epidemiology
- Diagnostics
- Antibiotic Resistance
- Mycology
- Virology
- Entomology / Parasitology
- Sexual Health
Descriptions of selected research projects (2005)
Title: Translating molecular epidemiology into information to improve infectious disease risk assessment and control
Researchers: Lyn Gilbert, Enrico Coiera (UNSW), Philip Giffard (QUT), Vitali Sintchenko, Fanrong Kong
Funded by the NH&MRC, this project will develop methods for genotyping of the important bacterial pathogens, pneumococcus and group B streptococcus. Patterns of microevolution or recombination that correlate with virulence will be investigated by identifying combinations of genetic profiles and machine learning algorithms developed and applied to translate genetic, clinical and epidemiological data into useful, timely and accessible clinical decision support tools.
Title: Reverse line blot assay for rapid molecular typing of Bordetella pertussis in respiratory samples.
Researchers: Vitali Sintchenko, Lyn Gilbert
We hypothesise that B.pertussisDNA from PCR-positive clinical samples can be used to directly identify virulence gene variants in a multiplex PCR with a reverse line blot assay. This will allow surveillance of circulating B.pertussis strains and elucidate its molecular epidemiology and pathogenicity in vaccinated populations. A decision support tool will be developed to assist clinicians and public health practitioners with interpretation and follow-up of molecular typing results and improve public health control measures.
Title: Arboviruses in cold storage – can the common marsh mosquito, Coquillettidia linealis vertically transmit Ross River virus?
Researchers: Petrina H. Johnson* and Richard C. Russell
The survival of Ross River virus (RRv) during periods of mosquito vector inactivity is important in arbovirus ecology in temperate Australia. Vertical transmission is a likely survival mechanism with infection of eggs and larvae. Coquillettidia linealis is a major pest species and vector of RR virus in NSW. The aim of this project is to examine the ability of Cq. linealis to remain dormant during winter and vertically transmit RRv.
Title: Increases in Norovirus Gastroenteritis in Australia in 2004.
Researchers: Belinda Herring, Joanne MacRae, Neisha Jeoffreys, and Dominic Dwyer in collaboration with Queensland Health Scientific Services
There was a sharp increase in the number of outbreaks of norovirus gastroenteritis 2004. To determine whether this was due to a new virus variant, reverse transcriptase (RT)-PCR and sequencing of the gene, pol, was performed on samples collected in 2000 and 2004. All norovirus strains belonged to genogroup II, and showed low genetic diversity but geographic and temporal clustering of pol sequences. Sequences from 2000 and 2004 were distinct, supporting the hypothesis that a relatively virulent norovirus variant had emerged. Title: Phylogenetic Analysis of Ross River Virus in Australia
Researchers: Belinda Herring, Katrina Patsouris, Stephen Doggett, Richard Russell and Dominic Dwyer.
Ross River virus (RRv) is transmitted by mosquitoes to humans and other vertebrate hosts throughout Australia and the South Pacific and causes fatigue, rash, fever and joint pain. Genetic evolution of RRV in Australia was investigated to determine if there were temporal, geographic or mosquito species-specific genetic differences in circulating viral variants.
Title: Molecular Methods for Resistance Detection in Gram-negative Bacteria.
Researchers: Lee Thomas, Jon Iredell.
High levels of antibiotic use are associated with increased antibiotic resistance in the microflora. Acquisition of novel resistance genes has been demonstrated by the recent discovery, at Westmead, of the first carbapenem-resistant enteric Gram-negative bacteria in Australia, conferred by a highly mobile gene ( imp-4) . Molecular survey tools for emerging as well as common resistance genes are being developed to screen for and identify resistance genes more quickly and inexpensively.
Title: A molecular-capsular-type prediction system for 90 Streptococcus pneumoniae serotypes using partial cpsA-cpsB sequencing and wzy - or wzx -specific PCR.
Researchers: Fanrong Kong and Gwendolyn L. Gilbert
We have developed a molecular capsular type (MCT) prediction system for all 90 Streptococcus pneumoniae serotypes, based on a combination of partial cpsA-cpsB sequencing and serotype(s)/group(s)-specific PCR. For initial screening we developed more practicable multiplex PCR and reverse line blot (RLB) hybridisation assay to identify the 23 serotypes included in the polysaccharide vaccine, with very promising results.
Title: Molecular epidemiology of group B streptococcus (GBS) based on complex genotyping system.
Researchers: Lyn Gilbert, Fanrong Kong
Our GBS fingerprinting system identifies a) molecular serotype (MS); b) surface protein gene profiles; c) 7 mobile genetic elements; d) 9 antibiotic resistance (AR) related markers and e) C beta sequence types. Based on genotyping of >1000 GBS isolates from 8 countries, we have identified significant differences in distribution of genotypes between different types of GBS disease and vaginal colonising strains and AR markers between geographic areas and GBS genotypes. A nalysis of molecular, clinical and epidemiological data using machine-learning algorithms will provide the basis for risk assessment in GBS carriers.
Title: Reduced penicillin susceptibility in the Treponema genus
researchers: Neisha Jeoffreys Jo Backhouse, Greg James, Lyn Gilbert.
Treponema pallidum subspecies pertenue ( T.p.pertenue ), the causative agent of yaws, is currently effectively treated with penicillin. Recently, a possible reduction in penicillin susceptibility has been identified in Papua New Guinea (PNG) with cases of persistent infection. This study aimed to confirm this using an animal model, PBP profiling and gene sequencing.
Title: Molecular typing of M. tuberculosis in New South Wales
Researchers: Peter Jelfs, Taryn Crighton, Vitali Sintchenko, Lyn Gilbert
Since early 2003, molecular typing has been performed on all new isolates of M.tuberculosis received at the Mycobacterium Reference Laboratory using two PCR based methods – spoligotyping and mycobacterial interspersed repetitive unit (MIRU) typing. IS6110 RFLP further differentiates isolates indistinguishable by these methods. Of 420 sequential isolates of M.tuberculosis , 65% and 42% were clustered by spoligotyping and MIRU typing, respectively, individually and 25% by both combined. Eight clusters involving 20 isolates (5%) were identified and investigated. More details about research activities will be added soon.
