Please send in your queries, CV and preferred project titles to students@uqccr.uq.edu.au.

Tracking the antibiotic resistant genes through plasmid replicons

Type of project: Honours/PhD/MPhil

Supervisor: Dr Hanna Sidjabat

Project Description: Plasmids carrying antibiotic resistance genes can be typed by its replicons, origin of plasmid replication. To understand the reservoir of antibiotic resistance genes, it can also be done by typing the replicons of bacterial plasmids from the environment.

Analysis of genome and plasmid sequences of NDM producing bacteria

Type of project: Honours/PhD/MPhil

Supervisor: Dr Hanna Sidjabat

Project Description: NDM, a newly described carbapenemase was first described in 2009. It has spread worldwide and been reported in nearly 20 species. Its rapidity to spread is remarkable. The understanding of genome and plasmid of NDM producers will help to explain the spread of NDM gene.

Molecular epidemiology of antibiotic resistance genes in Gram-negative bacteria

Type of project: Honours/PhD/MPhil

Supervisor: Dr Hanna Sidjabat

Project Description: A particular clone of A. baumannii, ST92 is responsible in carbapenemase resistance of this species. The chromosomal location of carbapenemase gene in A. baumannii, makes it predominant clone in Australia and worldwide. Whether it is the same phenomenon in other species of bacteria (E. coli, K. pneumoniae, E. cloacae, many others) it is not well explored in Queensland and Australia.

Investigation of Clostridium difficile strains prevalent in Queensland using genomic and proteomic approaches

Type of project: Honours

Supervisor: Professor David Paterson

Project Description: Clostridium difficile strains prevalent in Queensland will be investigated applying PCR based methods such as ribotyping and detection of clostridial toxin genes. Strains of known ribotype and toxin status will further be analysed for protein expression patterns using mass spectrometry. 

Bacterial interference and biofilm formation of pathogens from cystic fibrosis patients

Type of project: Honours

Supervisor: Dr Hanna Sidjabat , Dr Eva Grahn Hakansson (Umea University)

Project Description: Biofilm is an aggregate of microorganisms in which cells adhere to each other on a surface. Biofilm often occurs on the chronic colonisation of human tissues and persistence in implanted medical devices. Many antibiotics can not eradicate dense biofilms. P. aeruginosa is an important nosocomial pathogen especially among cystic fibrosis patients. In this project, student will perform biofilm formation by various strains of P. aeruginosa and its interaction with potential use of oral normal flora to observe the bacterial interference in the respiratory tract. 

Characterisation of bacterial genome and proteome of commensal bacteria from upper respiratory tract

Type of project: Honours

Supervisor: Dr Hanna Sidjabat , Professor Anders Cervin

Project Description: Chronic rhinosinusitis (CRS) cause significant reduction of quality of life which affects middle-aged adults. CRS affects 8-10% of western-population and can strike indiscriminately. Commensal bacteria or commensals colonising upper respiratory tract (URT) protect the URT from the invasion by respiratory pathogens. A sub-set of commensal bacteria will be analysed for the bacterial genome and proteome to understand their protective properties to the mucosal membrane. Bacterial DNA will be sequenced using whole-genome sequencing. Protein will be extracted, purified and quantified. Bacterial protein will be digested with trypsin into peptides and desalted, which then subsequently analysed in the liquid-chromatography mass spectrometry (LC-MS/MS). Genes and proteins with protective properties to the mucosal membrane will be studied in more detail.