Postdoctoral and Postgraduate Researchers in the Infectious Disease Research Centre

Postdoctoral and Postgraduate Researchers

Postdocs
	Sara Burgess Sara is working in the mEpiLab and is working on a project with PhD student Leah Toombs-Ruane funded by the Health Reseach Council, which aims to address the question “is the family pet a risk factor for multidrug resistant bacterial infections?". In addition, Sara will explore if the environment plays a role in the transmission and epidemiology of antimicrobial resistance by members of the Enterobacteriaceae family in New Zealand.
	Ji Zhang Ji is working at mEpilab, he is involved in a number of projects base on Bioinformatics and Computational Biology. Ji has a medical background and worked in China CDC for three years in the areas of genomics, molecular epidemiology and bioinformatics. Ji have a broad range of research interest including molecular epidemiology, genomics, evolution and ecology of pathogens, as well as phylogenetics, host-pathogen interaction and bioinformatics.
	David Wilkinson David is working at mEpilab, he is involved in a number of projects including the study of Campylobacter and Leptospira in domestic and wild animals. David has a particular interest in the One Health framework, and the combination of classical Microbiology, Genetics and state-of-the-art Genomics to study the evolution and epidemiology of disease-causing microorganisms.
	Tim Vaughan Tim is working on an Allan Wilson Centre funded project entitled: "Integrating models of evolutionary ancestry and the transmission of infectious disease". This is a joint position between Nigel French's ^mEpiLab team within IDReC and Alexei Drummond's Computational Evolution Group at the University of Auckland. Bacterial and viral pathogens often undergo extremely rapid evolutionary changes over very short time scales---even during the course of a single infection. Tim is using mathematical and computational models to characterize this evolution and to determine how it relates to between-host transmission events and the demographic history of the host population.
	Honour McCann Honour McCann is working in Paul Rainey's lab on a Ministry of Science and Innovation funded project examining the evolution of virulence in the kiwifruit pathogen Pseudomonas syringae pv. actinidiae (Psa). This work is performed in collaboration with the New Zealand Institute for Plant and Food Research. Virulence in P. syringae is thought to be largely determined by the injection of bacterial virulence proteins directly into host cells by the type 3 secretion system. Comparative genomic analysis has revealed extensive variation in type 3 secreted effector repertoires between Psa isolated prior to and during the recent global outbreak of kiwifruit canker disease. Honour's work will establish which outbreak-specific genes are linked with differences in virulence and host specificity exhibited by Psa, and provide targets for the development of disease resistance strategies in new cultivars of kiwifruit.
Postgrads
	Reed Hanrc ^mEpiLab Reed work for his PhD is focused on modeling infectious diseases of wildlife, specifically bats and is broken into two parts. The first involves spatial-temporal modelling of Filoviruses in central and western Africa to investigate potential sylvatic viral maintenance within the Chiropteran community. The other half of my project concerns the White-nose Syndrome outbreak among bats in North America and using models to evaluate the metabolic consequences of fungal infection during hibernation.
	Kate Richards Institute of Fundamental Sciences / EpiCentre Kate's PhD thesis is entitled "Disease mapping for veterinary epidemiology" and she is being supervised by Martin Hazelton (IFS) and Mark Stevenson (EpiCentre, IVABS). Kate's research is focused on developing a series of methods for use in analysing veterinary epidemiological data. She is looking at methods of spatial-temporal modelling when data quality is poor, as well as identifying areas of possible under reporting of disease. She is also interested in looking at the evaluation of intervention strategies, and is aiming to provide a set of guidelines for model diagnostics for a range of spatial resolutions.
	Karen McCulloch Institute of Natural and Mathematical Sciences Karen is developing and analysing mathematical models that describe the spread of an infectious disease. Karen's models take account of the spatial structure of the host population, through representing it on a network and in a diffusion-based context. She will be comparing these two approaches and assessing their strengths and weaknesses. Karen is based on the Albany campus where she is supervised by Mick Roberts.
	Andrea Babylon Institute of Natural and Mathematical Sciences Andrea is developing a multi-species mathematical model to describe the spread and interaction of leptospirosis between human and animal hosts. Andrea will use the model to exlore how the interaction of the disease between human and animal hosts changes the disease dynamic, and how the bacteria changes the dynamics of the host populations. She will also be assessing the effect of vaccinating animals to prevent transmission of the disease to human hosts. The model will be parameterised with data appropriate for leptospirosis in New Zealand. Andrea is based on the Albany campus where she is supervised by Mick Roberts.
	Springer Browne ^mEpiLab / MPI / MIA The title of Springer's PhD thesis is "A food chain approach to control of shigatoxigenic E. coli in New Zealand". He is being supervised by Nigel French, Anne Midwinter, Patrick Biggs, Jonathan Marshall, and Jackie Benschop (^mEpiLab), Adrian Cookson (AgResearch), and Helen Winters and Steve Hathaway (MPI). Springer's research focuses on improving the methods of detection for 7 of the most common shigatoxigenic E. coli (STEC), as well as understanding the risk factors and overall prevalence of STECs in New Zealand. STECs can cause serious and sometimes fatal disease in humans, and cattle are recognized as the main reservoir of the pathogen. The research is part of a collaborative effort with the government and meat industry to protect public health and New Zealand's meat export trade.
	Angela Cornelius ESR / ^mEpiLab The title of Angela’s PhD thesis is “Twenty first century tools for investigating human bacterial gastroenteritis”. She is being supervised by Stephen On (ESR), Patrick Biggs (^mEpiLab) and Nigel French (^mEpiLab). This project aims to develop tools, capability, and knowledge that will help elucidate the causes and sources of some currently undiagnosed gastroenteritis cases, thus enabling the development of appropriately targeted interventions. Andgela’s work will focus on the rapid and specific detection of Epsilonproteobacteria, a diverse group that includes the Campylobacter, Helicobacter and Arcobacter genera, in human stool samples.
	KomKiew Pinpamai IVABS / ^mEpiLab The title of Komkiew’s PhD is “Klebsiella pneumoniae in New Zealand sea lions”. KomKiew's research investigates the pathogenesis and virulence of a hypermucoviscous isolate of K. pneumoniae that causes septicaemia and meningitis with high mortality in sea lion pups. Komkiew is being supervised by Wendi Roe (IVABS), Keren Dittmer (IVABS) and Patrick Biggs (^mEpiLab).
	Samuel Bloomfield ^mEpiLab / ESR Samuel is working on a doctoral thesis entitled "Transmission and evolution of bacterial gastroenteritis outbreaks". He is being supervised by Jackie Benschop, Anne Midwinter, Patrick Biggs, Jonathan Marshall, Nigel French and David Hayman (mEpiLab), and Phillip Carter (ESR). The two largest causes of bacterial gastroenteritis in New Zealand are Campylobacter and Salmonella. Samuel is investigating outbreaks of Campylobacter and Salmonella, in an attempt to model their transmission and evolution. These models should help decrease the severity and incidence of bacterial gastroenteritis in New Zealand.
	Nelly Marquetoux EpiCentre / IVABS Nelly’s work focusses on the epidemiology of paratuberculosis in mixed species farms in New Zealand. Nelly’s PhD is supervised by Cord Heuer (EpiCentre), Peter Wilson (IVABS), Anne Ridler (IVABS), and Mark Stevenson (University of Melbourne). Nelly is analysing the contact pattern of livestock trade in New Zealand to assess the possibility of farm-to-farm transmission of paratuberculosis via animal movement. She is also investigating possible spatial spread from farm to farm via fecal contamination of neighbouring paddocks. This work involves social network analysis, molecular epidemiology and Bayesian analysis.As part of this project Nelly is developing a SIR mathematical model to simulate the spread of paratuberculosis in sheep with a focus on evaluating the effectiveness of different control strategies and the economic impact of ovine paratuberculosis.
	Leah Toombs-Ruane ^mEpiLab / IVABS Leah's project, funded by the Heath research Council of New Zealand, aims to address the question "is the family pet a risk factor for multidrug resistant bacterial infections?" The core supervisors for this project are Jackie Benschop, Nigel French, Patrick Biggs, and Anne Midwinter and Jonathan Marshall (mEpiLab). They will be joined by advisors from Massey University (Albany and Wellington), ESR, University of Otago, MPI, and Waitemata DHB. Antimicrobial resistance is an area of growing worldwide concern and this project aims to assess risk factors for community-associated resistant Gram-negative bacterial infections in people. The potential transmission of these multi-drug resistant genetics between humans and animals will also be investigated as part of this study. Leah's work will also include potential public health interventions, and modeling analysis of these to decrease multidrug resistant infections in the community.
	Mary van andel EpiCentre / MPI / CEBRA The title of Mary's thesis is "Novel applications of new animal demographic and animal movement data sources for enhancing investigation and management of exotic disease outbreaks.".
	Yuni Yupiana EpiCentre The title of Yuni's thesis is “Cross sectional study of leptospirosis in dairy cattle in New Zealand.”.
	Alicia Coupe IVABS / EpiCentre The title of Alicia's thesis is “Toxoplasma gondii in the Marine Environment in New Zealand”. This PhD project is being supervised by Wendi Roe (IVABS), Tim Carpenter (EpiCentre) and Larissa Howe (IVABS)
	Chris Compton EpiCentre The title of Chris's thesis is “Productive lifetime and causes of dairy cow wastage”. This industry-funded PhD project aims to define the patterns of culling and mortality, their causes and their economic impact This project will provide tools for farmers to benchmark culling and mortality performance and to estimate their financial consequences
	Arata Hidano EpiCentre The title of Arata's thesis is “Development a cost-effective approach to the elimination of bovine tuberculosis among livestock in New Zealand”. The control of bovine tuberculosis (bTB) in New Zealand has been successful, observing the huge reduction in the cattle herd prevalence from around 4% to 0.2% (as of 2014). However, the presnece of wildlife vector for bTB, brushtail possum, makes bTB elimintaion from NZ extremely difficult. It is therefore required to develop a cost-effective bTB control strategy in livestock. To answer this, my PhD project evaluates various bTB control strategy using a simulation modelling approach, considering a nation-wide stock movement between herds.
	Milan Gautam EpiCentre The title of Milan's thesis is “Epidemiology, economics and control of ovine Johne' s disease in New Zealand”. Estimate production loss caused by Johne's disease in sheep in NZ. Investigate potential virulence between MAP strains in sheep using Whole Genome Sequencing technique. Determine intra-herd distribution of faecal shedding of MAP using PCR technique. Validation of ELISA to predict high shedders in farms.
	Marie Moinet mEpiLab The title of Marie's thesis is “Molecular and Eco-epidemiology of leptospirosis at the wildlife - cattle -human interface in New Zealand". She is supervised by Jackie Benschop (mEpiLab), Julie Collins-Emerson (mEpiLab), David Wilkinson (mEpiLab), Danielle Aberdein (IVABS), Cord Heuer (EpiCentre), Emilie Vallée (EpiCentre), Peter Wilson (EpiCentre) and James Russell (University of Auckland). Marie is investigating the potential role of abundant wildlife species and the risk it poses for cattle and humans by determining the prevalence of Leptospira serovars, renal colonisation and urinary shedding in abundant wildlife species around farms. Using a multidisciplinary approach (disease ecology, spatial epidemiology, host pathology, microbiology and genomics) this project should give a new insight on leptospirosis transmission pathways and better inform control strategies.
	Aaron Yang EpiCentre The title of Aaron's thesis is “Veterinary Studies of Bovine Digital Dermatitis in Pasture-based Dairy System in New Zealand". We aim to develop a new statistical approach to model zero-inflated data with repeated measurements. We are investigating how common BDD lesions are across the country and propose control strategies. We are comparing two or three diagnostic tests to find out the most effective and economic friendly test in order to diagnose BDD on farm.
	Katja Isaken EpiCentre Katja is working on a project to find out "What makes a working farm dog excellent?" The project focuses on defining what high performance means in a working farm dog by asking farmers what qualities they value in their dogs and by measuring activity levels in the dogs over time, and correlating this with population and veterinary data. Once performance is defined, this can be used to measure the effect of interventions in diet, husbandry, veterinary treatments, etc. on the working ability of these dogs. Katja is being surpervised by Naomi Cogger (EpiCentre), Ngaio Beausoleil (IVABS), Nick Cave (IVABS) and Liz Norman (IVABS).